Title: R Interface for H2O Sparkling Water
Description: An extension package for 'sparklyr' that provides an R interface to
H2O Sparkling Water machine learning library (see <https://github.com/h2oai/sparkling-water> for more information).
Author: Jakub Hava [aut, cre],
Navdeep Gill [aut],
Erin LeDell [aut],
Michal Malohlava [aut],
JJ Allaire [aut],
H2O.ai [cph],
RStudio [cph]
Maintainer: Jakub Hava <jakub@h2o.ai>
Diff between rsparkling versions 0.2.18 dated 2019-01-30 and 0.2.19 dated 2020-01-28
rsparkling-0.2.18/rsparkling/R/h2o_context.R |only rsparkling-0.2.18/rsparkling/R/install_h2o.R |only rsparkling-0.2.18/rsparkling/R/sysdata.rda |only rsparkling-0.2.18/rsparkling/inst |only rsparkling-0.2.18/rsparkling/man |only rsparkling-0.2.18/rsparkling/tests/testthat |only rsparkling-0.2.19/rsparkling/DESCRIPTION | 8 - rsparkling-0.2.19/rsparkling/MD5 | 26 ---- rsparkling-0.2.19/rsparkling/NAMESPACE | 25 ---- rsparkling-0.2.19/rsparkling/R/package.R | 155 +------------------------- rsparkling-0.2.19/rsparkling/tests/testthat.R | 15 -- 11 files changed, 20 insertions(+), 209 deletions(-)
Title: Spatial Covariance Functions
Description: Spatial (cross-)covariance and related geostatistical tools: the
nonparametric (cross-)covariance function , the spline correlogram, the
nonparametric phase coherence function, local indicators of spatial
association (LISA), (Mantel) correlogram, (Partial) Mantel test.
Author: Ottar N. Bjornstad [aut, cre],
Jun Cai [ctb]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>
Diff between ncf versions 1.2-8 dated 2019-03-22 and 1.2-9 dated 2020-01-28
CHANGES | 2 + DESCRIPTION | 12 ++++---- MD5 | 60 ++++++++++++++++++++++---------------------- R/Sncf.R | 8 ++--- R/Sncf2D.R | 12 ++++---- R/correlog.R | 32 +++++++++++------------ R/lisa.R | 8 ++--- R/mSynch.R | 4 +- R/mantel-test.R | 10 +++---- R/spline-correlog.R | 8 ++--- R/spline-correlog2D.R | 4 +- R/utilities.R | 4 +- man/Sncf.Rd | 4 +- man/Sncf.srf.Rd | 4 +- man/Sncf2D.Rd | 4 +- man/correlog.Rd | 10 +++---- man/correlog.nc.Rd | 10 +++---- man/ff.filter.Rd | 4 +- man/lisa.Rd | 2 - man/lisa.nc.Rd | 4 +- man/mSynch.Rd | 2 - man/mantel.correlog.Rd | 4 +- man/mantel.test.Rd | 2 - man/partial.mantel.test.Rd | 6 ++-- man/plot.Sncf2D.Rd | 2 - man/plot.cc.offset.Rd | 2 - man/plot.correlog.Rd | 2 - man/plot.lisa.Rd | 4 +- man/plot.spline.correlog.Rd | 2 - man/spline.correlog.Rd | 6 ++-- man/spline.correlog2D.Rd | 4 +- 31 files changed, 122 insertions(+), 120 deletions(-)
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via Three. JAGS types of models may be fitted: 1) With explanatory variables only, boral fits independent column Generalized Linear Models (GLMs) to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui <fhui28@gmail.com>, with contributions from Wade Blanchard <wade.blanchard@anu.edu.au>
Maintainer: Francis Hui <fhui28@gmail.com>
Diff between boral versions 1.7 dated 2018-10-21 and 1.8 dated 2020-01-28
DESCRIPTION | 14 MD5 | 83 ++-- NAMESPACE | 18 R/auxilaryfunctions.R | 352 ----------------- R/boral.jags.R | 746 ++++++++++++------------------------- R/calclogLfunctions.R | 70 +-- R/checkfunctions.R |only R/getcorrelations.R | 209 +++++----- R/getmeasures.R | 26 - R/hpdintervals.R |only R/makejagsboralmodel.R | 521 +++++++++++++------------ R/makejagsboralnullmodel.R | 465 +++++++++++------------ R/plotboral.R |only R/predictfn.R |only R/simdatafunctions.R | 30 - R/summaryboral.R |only R/tidyboral.R |only R/unseenfunctions.R | 826 +++++++++++++++++++---------------------- build/partial.rdb |binary inst/NEWS.Rd | 19 man/about.lvs.Rd | 9 man/about.ssvs.Rd | 19 man/about.traits.Rd | 12 man/boral.Rd | 52 +- man/calc.condlogLik.Rd | 35 - man/calc.logLik.lv0.Rd | 31 - man/calc.marglogLik.Rd | 36 + man/calc.varpart.Rd | 16 man/coefsplot.Rd | 16 man/create.life.Rd | 30 - man/ds.residuals.Rd | 13 man/fitted.boral.Rd | 11 man/get.dic.Rd | 14 man/get.enviro.cor.Rd | 22 - man/get.hpdintervals.Rd | 21 - man/get.mcmcsamples.Rd | 17 man/get.measures.Rd | 25 - man/get.more.measures.Rd | 30 - man/get.residual.cor.Rd | 19 man/lvsplot.Rd | 11 man/make.jagsboralmodel.Rd | 36 - man/make.jagsboralnullmodel.Rd | 34 - man/plot.boral.Rd | 11 man/predict.boral.Rd | 35 + man/summary.boral.Rd | 10 man/tidyboral.Rd |only 46 files changed, 1748 insertions(+), 2196 deletions(-)
Title: Reliability Coefficients
Description: Derives point estimates with confidence intervals for Bennett et als S, Cohen's kappa, Conger's kappa, Fleiss' kappa, Gwet's AC, intraclass correlation coefficients, Krippendorff's alpha, Scott's pi, the standard error of measurement, and weighted kappa.
Author: Riccardo LoMartire
Maintainer: Riccardo LoMartire <lomartire@kth.se>
Diff between rel versions 1.4.0 dated 2020-01-19 and 1.4.1 dated 2020-01-28
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 4 ++++ R/bags.R | 2 +- R/ckap.R | 4 ++-- R/gac.R | 4 ++-- R/kra.R | 14 +++++++------- R/spi.R | 4 ++-- 8 files changed, 28 insertions(+), 24 deletions(-)
Title: Tidy Data and 'Geoms' for Bayesian Models
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models
('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided
to help extract tidy data frames of draws from Bayesian models and that generate point
summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for
common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus
densities), and fit curves with multiple, arbitrary uncertainty bands.
Author: Matthew Kay [aut, cre],
Timothy Mastny [ctb]
Maintainer: Matthew Kay <mjskay@umich.edu>
Diff between tidybayes versions 1.1.0 dated 2019-06-02 and 2.0.1 dated 2020-01-28
tidybayes-1.1.0/tidybayes/R/geom_eyeh.R |only tidybayes-1.1.0/tidybayes/R/geom_grouped_violin.R |only tidybayes-1.1.0/tidybayes/R/geom_grouped_violinh.R |only tidybayes-1.1.0/tidybayes/R/geom_halfeyeh.R |only tidybayes-1.1.0/tidybayes/man/geom_halfeyeh.Rd |only tidybayes-1.1.0/tidybayes/tests/figs/geom-eye |only tidybayes-1.1.0/tidybayes/tests/figs/geom-interval/grouped-intervals-reverse-order.svg |only tidybayes-1.1.0/tidybayes/tests/figs/geom-interval/grouped-intervals-stat-mode-hdi.svg |only tidybayes-1.1.0/tidybayes/tests/figs/geom-interval/grouped-intervals-stat-reverse-order.svg |only tidybayes-1.1.0/tidybayes/tests/figs/geom-lineribbon/one-group-stat-lineribbon-mean-qi.svg |only tidybayes-1.1.0/tidybayes/tests/figs/geom-lineribbon/one-group-stat-lineribbon-reverse-order.svg |only tidybayes-1.1.0/tidybayes/tests/figs/geom-lineribbon/two-group-stat-lineribbons-grouped-by-color.svg |only 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tidybayes-2.0.1/tidybayes/tests/testthat/test.scales.R |only tidybayes-2.0.1/tidybayes/tests/testthat/test.spread_draws.R | 2 tidybayes-2.0.1/tidybayes/tests/testthat/test.stat_cdfinterval.R |only tidybayes-2.0.1/tidybayes/tests/testthat/test.stat_dist_slabinterval.R |only tidybayes-2.0.1/tidybayes/tests/testthat/test.stat_eye.R |only tidybayes-2.0.1/tidybayes/tests/testthat/test.stat_sample_slabinterval.R |only tidybayes-2.0.1/tidybayes/tests/testthat/test.tidy_draws.R | 54 tidybayes-2.0.1/tidybayes/vignettes/freq-uncertainty-vis.Rmd |only tidybayes-2.0.1/tidybayes/vignettes/slabinterval.Rmd |only tidybayes-2.0.1/tidybayes/vignettes/slabinterval_family.png |only tidybayes-2.0.1/tidybayes/vignettes/tidy-brms.Rmd | 247 - tidybayes-2.0.1/tidybayes/vignettes/tidy-rstanarm.Rmd | 127 tidybayes-2.0.1/tidybayes/vignettes/tidybayes-residuals.Rmd | 127 tidybayes-2.0.1/tidybayes/vignettes/tidybayes.Rmd | 183 210 files changed, 10318 insertions(+), 9264 deletions(-)
Title: Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output
Description: Functions for the input/output and visualization of
medical imaging data that follow either the 'ANALYZE', 'NIfTI' or 'AFNI'
formats. This package is part of the Rigorous Analytics bundle.
Author: Brandon Whitcher [aut, cre],
Volker Schmid [aut],
Andrew Thornton [aut],
Karsten Tabelow [ctb],
Jon Clayden [ctb],
John Muschelli [aut]
Maintainer: Brandon Whitcher <bwhitcher@gmail.com>
Diff between oro.nifti versions 0.9.1 dated 2017-10-26 and 0.10.1 dated 2020-01-28
oro.nifti-0.10.1/oro.nifti/DESCRIPTION | 61 + oro.nifti-0.10.1/oro.nifti/MD5 | 392 ++++++------ oro.nifti-0.10.1/oro.nifti/NAMESPACE | 11 oro.nifti-0.10.1/oro.nifti/NEWS.md | 20 oro.nifti-0.10.1/oro.nifti/R/Operators.R | 2 oro.nifti-0.10.1/oro.nifti/R/afniS4.R | 11 oro.nifti-0.10.1/oro.nifti/R/analyzeS4.R | 8 oro.nifti-0.10.1/oro.nifti/R/anlz_Operators.R | 2 oro.nifti-0.10.1/oro.nifti/R/aux_file.R | 14 oro.nifti-0.10.1/oro.nifti/R/bitpix.R | 8 oro.nifti-0.10.1/oro.nifti/R/cal_max.R | 14 oro.nifti-0.10.1/oro.nifti/R/cal_min.R | 14 oro.nifti-0.10.1/oro.nifti/R/cal_units.R | 10 oro.nifti-0.10.1/oro.nifti/R/coerce.R | 1 oro.nifti-0.10.1/oro.nifti/R/compressed.R | 6 oro.nifti-0.10.1/oro.nifti/R/convert_anlz.R | 4 oro.nifti-0.10.1/oro.nifti/R/convert_nifti.R | 2 oro.nifti-0.10.1/oro.nifti/R/data_type.R | 14 oro.nifti-0.10.1/oro.nifti/R/datatype.R | 21 oro.nifti-0.10.1/oro.nifti/R/db_name.R | 14 oro.nifti-0.10.1/oro.nifti/R/descrip.R | 8 oro.nifti-0.10.1/oro.nifti/R/dim_.R | 20 oro.nifti-0.10.1/oro.nifti/R/dim_info.R | 6 oro.nifti-0.10.1/oro.nifti/R/dim_un0.R | 6 oro.nifti-0.10.1/oro.nifti/R/exp_date.R | 6 oro.nifti-0.10.1/oro.nifti/R/exp_time.R | 6 oro.nifti-0.10.1/oro.nifti/R/extender.R | 6 oro.nifti-0.10.1/oro.nifti/R/extents.R | 8 oro.nifti-0.10.1/oro.nifti/R/field_skip.R | 10 oro.nifti-0.10.1/oro.nifti/R/funused1.R | 6 oro.nifti-0.10.1/oro.nifti/R/funused2.R | 6 oro.nifti-0.10.1/oro.nifti/R/funused3.R | 6 oro.nifti-0.10.1/oro.nifti/R/generated.R | 6 oro.nifti-0.10.1/oro.nifti/R/glmax.R | 8 oro.nifti-0.10.1/oro.nifti/R/glmin.R | 8 oro.nifti-0.10.1/oro.nifti/R/hist_un0.R | 6 oro.nifti-0.10.1/oro.nifti/R/hkey_un0.R | 10 oro.nifti-0.10.1/oro.nifti/R/img_data.R | 16 oro.nifti-0.10.1/oro.nifti/R/img_length.R |only oro.nifti-0.10.1/oro.nifti/R/intent_code.R | 10 oro.nifti-0.10.1/oro.nifti/R/intent_name.R | 10 oro.nifti-0.10.1/oro.nifti/R/intent_p1.R | 10 oro.nifti-0.10.1/oro.nifti/R/intent_p2.R | 10 oro.nifti-0.10.1/oro.nifti/R/intent_p3.R | 10 oro.nifti-0.10.1/oro.nifti/R/is.R | 2 oro.nifti-0.10.1/oro.nifti/R/magic.R | 6 oro.nifti-0.10.1/oro.nifti/R/niftiImage_class.R |only oro.nifti-0.10.1/oro.nifti/R/niftiS4.R | 10 oro.nifti-0.10.1/oro.nifti/R/nifti_assign.R | 1 oro.nifti-0.10.1/oro.nifti/R/nii2oro.R | 4 oro.nifti-0.10.1/oro.nifti/R/omax.R | 6 oro.nifti-0.10.1/oro.nifti/R/omin.R | 6 oro.nifti-0.10.1/oro.nifti/R/orient.R | 6 oro.nifti-0.10.1/oro.nifti/R/origin.R | 59 + oro.nifti-0.10.1/oro.nifti/R/oro2nii.R | 2 oro.nifti-0.10.1/oro.nifti/R/patient_id.R | 10 oro.nifti-0.10.1/oro.nifti/R/pixdim.R | 38 + oro.nifti-0.10.1/oro.nifti/R/plot.R | 60 + oro.nifti-0.10.1/oro.nifti/R/qform_code.R | 10 oro.nifti-0.10.1/oro.nifti/R/qoffset_x.R | 10 oro.nifti-0.10.1/oro.nifti/R/qoffset_y.R | 10 oro.nifti-0.10.1/oro.nifti/R/qoffset_z.R | 10 oro.nifti-0.10.1/oro.nifti/R/quatern_b.R | 10 oro.nifti-0.10.1/oro.nifti/R/quatern_c.R | 10 oro.nifti-0.10.1/oro.nifti/R/quatern_d.R | 10 oro.nifti-0.10.1/oro.nifti/R/readS4.R | 81 +- oro.nifti-0.10.1/oro.nifti/R/regular.R | 8 oro.nifti-0.10.1/oro.nifti/R/scannum.R | 6 oro.nifti-0.10.1/oro.nifti/R/scl_inter.R | 10 oro.nifti-0.10.1/oro.nifti/R/scl_slope.R | 10 oro.nifti-0.10.1/oro.nifti/R/session_error.R | 14 oro.nifti-0.10.1/oro.nifti/R/sform_code.R | 10 oro.nifti-0.10.1/oro.nifti/R/sizeof_hdr.R | 45 + oro.nifti-0.10.1/oro.nifti/R/slice.R | 7 oro.nifti-0.10.1/oro.nifti/R/slice_code.R | 10 oro.nifti-0.10.1/oro.nifti/R/slice_duration.R | 10 oro.nifti-0.10.1/oro.nifti/R/slice_end.R | 10 oro.nifti-0.10.1/oro.nifti/R/slice_overlay.R | 3 oro.nifti-0.10.1/oro.nifti/R/slice_start.R | 10 oro.nifti-0.10.1/oro.nifti/R/smax.R | 6 oro.nifti-0.10.1/oro.nifti/R/smin.R | 6 oro.nifti-0.10.1/oro.nifti/R/srow_x.R | 10 oro.nifti-0.10.1/oro.nifti/R/srow_y.R | 10 oro.nifti-0.10.1/oro.nifti/R/srow_z.R | 10 oro.nifti-0.10.1/oro.nifti/R/start_field.R | 6 oro.nifti-0.10.1/oro.nifti/R/toffset.R | 6 oro.nifti-0.10.1/oro.nifti/R/unused1.R | 6 oro.nifti-0.10.1/oro.nifti/R/verified.R | 6 oro.nifti-0.10.1/oro.nifti/R/views.R | 6 oro.nifti-0.10.1/oro.nifti/R/vols_added.R | 10 oro.nifti-0.10.1/oro.nifti/R/vox_offset.R | 14 oro.nifti-0.10.1/oro.nifti/R/vox_units.R | 10 oro.nifti-0.10.1/oro.nifti/R/voxdim.R | 8 oro.nifti-0.10.1/oro.nifti/R/writeS4.R | 16 oro.nifti-0.10.1/oro.nifti/R/xyzt_units.R | 10 oro.nifti-0.10.1/oro.nifti/R/zero_trans.R | 4 oro.nifti-0.10.1/oro.nifti/R/zzz.R | 22 oro.nifti-0.10.1/oro.nifti/R/zzz_niftiImage.R |only oro.nifti-0.10.1/oro.nifti/man/afni-class.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/anlz-class.Rd | 4 oro.nifti-0.10.1/oro.nifti/man/anlz-nifti-ops.Rd | 3 oro.nifti-0.10.1/oro.nifti/man/anlz.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/audit_trail.Rd | 40 - oro.nifti-0.10.1/oro.nifti/man/aux_file-methods.Rd | 15 oro.nifti-0.10.1/oro.nifti/man/bitpix-methods.Rd | 12 oro.nifti-0.10.1/oro.nifti/man/cal_max-methods.Rd | 29 oro.nifti-0.10.1/oro.nifti/man/cal_min-methods.Rd | 16 oro.nifti-0.10.1/oro.nifti/man/cal_units-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/coerce-methods.Rd | 4 oro.nifti-0.10.1/oro.nifti/man/compressed-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/convert_anlz.Rd | 4 oro.nifti-0.10.1/oro.nifti/man/convert_nifti.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/data_type-methods.Rd | 16 oro.nifti-0.10.1/oro.nifti/man/datatype-methods.Rd | 5 oro.nifti-0.10.1/oro.nifti/man/db_name-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/descrip-methods.Rd | 18 oro.nifti-0.10.1/oro.nifti/man/dim_-methods.Rd | 5 oro.nifti-0.10.1/oro.nifti/man/dim_info-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/dim_un0-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/exp_date-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/exp_time-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/extender-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/extents-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/field_skip-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/funused1-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/funused2-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/funused3-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/generated-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/glmax-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/glmin-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/hist_un0-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/hkey_un0-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/image-methods.Rd | 40 - oro.nifti-0.10.1/oro.nifti/man/img_data-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/img_length.Rd |only oro.nifti-0.10.1/oro.nifti/man/intent_code-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/man/intent_name-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/man/intent_p1-methods.Rd | 23 oro.nifti-0.10.1/oro.nifti/man/intent_p2-methods.Rd | 10 oro.nifti-0.10.1/oro.nifti/man/intent_p3-methods.Rd | 10 oro.nifti-0.10.1/oro.nifti/man/internalImage-class.Rd |only oro.nifti-0.10.1/oro.nifti/man/is_anlz.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/magic-methods.Rd | 21 oro.nifti-0.10.1/oro.nifti/man/nifti-class.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/nifti.Rd | 11 oro.nifti-0.10.1/oro.nifti/man/niftiImage-class.Rd |only oro.nifti-0.10.1/oro.nifti/man/niftiops.Rd | 3 oro.nifti-0.10.1/oro.nifti/man/omax-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/omin-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/orient-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/origin-methods.Rd | 21 oro.nifti-0.10.1/oro.nifti/man/orthographic-methods.Rd | 81 ++ oro.nifti-0.10.1/oro.nifti/man/overlay-methods.Rd | 159 ++++ oro.nifti-0.10.1/oro.nifti/man/patient_id-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/pixdim-methods.Rd | 8 oro.nifti-0.10.1/oro.nifti/man/qform_code-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/man/qoffset_x-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/man/qoffset_y-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/man/qoffset_z-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/man/quatern_b-methods.Rd | 23 oro.nifti-0.10.1/oro.nifti/man/quatern_c-methods.Rd | 10 oro.nifti-0.10.1/oro.nifti/man/quatern_d-methods.Rd | 10 oro.nifti-0.10.1/oro.nifti/man/read_afni.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/read_anlz.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/read_nifti.Rd | 14 oro.nifti-0.10.1/oro.nifti/man/regular-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/scannum-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/scl_inter-methods.Rd | 16 oro.nifti-0.10.1/oro.nifti/man/scl_slope-methods.Rd | 16 oro.nifti-0.10.1/oro.nifti/man/session_error-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/sform_code-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/man/sizeof_hdr-methods.Rd | 13 oro.nifti-0.10.1/oro.nifti/man/slice-methods.Rd | 43 + oro.nifti-0.10.1/oro.nifti/man/slice_code-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/man/slice_duration-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/man/slice_end-methods.Rd | 25 oro.nifti-0.10.1/oro.nifti/man/slice_overlay-methods.Rd | 159 ++++ oro.nifti-0.10.1/oro.nifti/man/slice_start-methods.Rd | 25 oro.nifti-0.10.1/oro.nifti/man/smax-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/smin-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/srow_x-methods.Rd | 25 oro.nifti-0.10.1/oro.nifti/man/srow_y-methods.Rd | 10 oro.nifti-0.10.1/oro.nifti/man/srow_z-methods.Rd | 10 oro.nifti-0.10.1/oro.nifti/man/start_field-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/toffset-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/man/unused1-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/verified-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/views-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/vols_added-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/vox_offset-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/man/vox_units-methods.Rd | 2 oro.nifti-0.10.1/oro.nifti/man/voxdim.Rd | 6 oro.nifti-0.10.1/oro.nifti/man/write_afni-methods.Rd | 5 oro.nifti-0.10.1/oro.nifti/man/write_anlz.Rd | 19 oro.nifti-0.10.1/oro.nifti/man/write_nifti.Rd | 57 + oro.nifti-0.10.1/oro.nifti/man/xyzt_units-methods.Rd | 17 oro.nifti-0.10.1/oro.nifti/tests/testthat/test_anlz.R | 71 ++ oro.nifti-0.10.1/oro.nifti/tests/testthat/test_nifti.R |only oro.nifti-0.10.1/oro.nifti/tests/testthat/test_nii2oro.R |only oro.nifti-0.10.1/oro.nifti/tests/testthat/test_sizeof_hdr.R | 14 oro.nifti-0.9.1/oro.nifti/inst/doc |only oro.nifti-0.9.1/oro.nifti/tests/Examples |only 202 files changed, 2070 insertions(+), 852 deletions(-)
Title: A Test Environment for HTTP Requests
Description: Testing and documenting code that communicates with remote servers
can be painful. Dealing with authentication, server state,
and other complications can make testing seem too costly to
bother with. But it doesn't need to be that hard. This package enables one
to test all of the logic on the R sides of the API in your package without
requiring access to the remote service. Importantly, it provides three
contexts that mock the network connection in different ways, as well as
testing functions to assert that HTTP requests were---or were
not---made. It also allows one to safely record real API responses to use as
test fixtures. The ability to save responses and load them offline also
enables one to write vignettes and other dynamic documents that can be
distributed without access to a live server.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest versions 3.2.2 dated 2018-12-07 and 3.3.0 dated 2020-01-28
DESCRIPTION | 14 ++++----- MD5 | 50 ++++++++++++++++----------------- NEWS.md | 9 +++++ R/capture-requests.R | 35 +++++------------------ R/expect-header.R | 9 +++-- R/find-redactor.R | 8 ++++- R/trace.R | 7 ++++ build/vignette.rds |binary inst/WORDLIST | 19 ++++++++---- inst/doc/redacting.Rmd | 2 - inst/doc/redacting.html | 2 - man/capture_requests.Rd | 25 ++++++---------- man/expect_header.Rd | 7 +++- man/expect_json_equivalent.Rd | 9 ++++- man/fake_response.Rd | 9 ++++- man/httptest.Rd | 1 man/public.Rd | 8 ++--- man/skip_if_disconnected.Rd | 6 ++- man/with_trace.Rd | 9 ++++- tests/testthat/helper.R | 7 ++++ tests/testthat/test-capture-requests.R | 25 +++++++--------- tests/testthat/test-expect-header.R | 9 +++++ tests/testthat/test-find-redactor.R | 38 ++++++++++++++++++------- tests/testthat/test-mock-api.R | 5 +-- tests/testthat/test-redact.R | 7 +--- vignettes/redacting.Rmd | 2 - 26 files changed, 190 insertions(+), 132 deletions(-)
Title: Geom for Logo Sequence Plots
Description: Visualize sequences in (modified) logo plots. The design choices
used by these logo plots allow sequencing data to be more easily analyzed.
Because it is integrated into the 'ggplot2' geom framework, these logo plots
support native features such as faceting.
Author: Heike Hofmann [aut],
Eric Hare [aut, cre],
GGobi Foundation [aut]
Maintainer: Eric Hare <eric@oaiti.org>
Diff between gglogo versions 0.1.4 dated 2019-06-28 and 0.1.5 dated 2020-01-28
gglogo-0.1.4/gglogo/data/aacids.rda |only gglogo-0.1.5/gglogo/DESCRIPTION | 15 +- gglogo-0.1.5/gglogo/MD5 | 44 +++--- gglogo-0.1.5/gglogo/NAMESPACE | 14 +- gglogo-0.1.5/gglogo/R/alphabet.r | 11 - gglogo-0.1.5/gglogo/R/logos.r | 144 ++++++++++++++-------- gglogo-0.1.5/gglogo/R/position.r | 4 gglogo-0.1.5/gglogo/R/text.r | 3 gglogo-0.1.5/gglogo/build/vignette.rds |binary gglogo-0.1.5/gglogo/data/aacids.RData |only gglogo-0.1.5/gglogo/inst/cluster.r | 4 gglogo-0.1.5/gglogo/inst/doc/gglogo-alphabet.R | 24 +-- gglogo-0.1.5/gglogo/inst/doc/gglogo-alphabet.Rmd | 11 - gglogo-0.1.5/gglogo/inst/doc/gglogo-alphabet.html | 69 ++++++---- gglogo-0.1.5/gglogo/man/calcInformation.Rd | 25 ++- gglogo-0.1.5/gglogo/man/createPolygons.Rd | 3 gglogo-0.1.5/gglogo/man/geom_logo.Rd | 24 ++- gglogo-0.1.5/gglogo/man/ggfortify.Rd | 7 - gglogo-0.1.5/gglogo/man/letterObject.Rd | 3 gglogo-0.1.5/gglogo/man/letterToPolygon.Rd | 11 + gglogo-0.1.5/gglogo/man/position_logo.Rd | 4 gglogo-0.1.5/gglogo/man/splitSequence.Rd | 4 gglogo-0.1.5/gglogo/man/stat_logo.Rd | 16 +- gglogo-0.1.5/gglogo/vignettes/gglogo-alphabet.Rmd | 11 - 24 files changed, 275 insertions(+), 176 deletions(-)
Title: Test and Item Analysis via Shiny
Description: Interactive shiny application for analysis of educational tests and
their items.
Author: Patricia Martinkova [aut, cre],
Adela Hladka [aut],
Ondrej Leder [ctb],
Jakub Houdek [ctb],
Lubomir Stepanek [ctb],
Tomas Jurica [ctb],
Jana Vorlickova [ctb],
Jan Netik [ctb]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>
Diff between ShinyItemAnalysis versions 1.3.1 dated 2019-06-26 and 1.3.2 dated 2020-01-28
DESCRIPTION | 15 MD5 | 154 NAMESPACE | 17 NEWS | 162 R/DDplot.R | 206 - R/DistractorAnalysis.R | 87 R/HCI.R | 14 R/HCIkey.R | 8 R/HCItest.R | 14 R/ItemAnalysis.R | 145 R/LearningToLearn.R |only R/Logistik_edited.R |only R/dataMedical.R | 44 R/dataMedicalgraded.R | 33 R/dataMedicalkey.R | 23 R/dataMedicaltest.R | 29 R/difLogistic_edited.R |only R/difMH_edited.R |only R/difSIBTEST_edited.R |only R/gDisrim.R | 61 R/ggWrightMap.R | 52 R/onAttach.R |only R/plotAdjacent.R | 94 R/plotCumulative.R | 171 R/plotDIFLogistic.R | 282 - R/plotDIFirt.R | 202 R/plotDistractorAnalysis.R | 125 R/plotMultinomial.R | 87 R/print_Logistic_edited.R |only R/startShinyItemAnalysis.R | 8 R/theme_app.R | 32 README.md | 9 data/HCI.rda |binary data/HCIkey.rda |binary data/HCItest.rda |binary data/LearningToLearn.rda |only data/dataMedical.rda |binary data/dataMedicalgraded.rda |binary data/dataMedicalkey.rda |binary data/dataMedicaltest.rda |binary inst/CITATION | 12 inst/shiny-examples/ShinyItemAnalysis/packages.sty | 12 inst/shiny-examples/ShinyItemAnalysis/reporthtml.Rmd | 770 ++- inst/shiny-examples/ShinyItemAnalysis/reportpdf.Rmd | 802 ++- inst/shiny-examples/ShinyItemAnalysis/server.R | 243 - inst/shiny-examples/ShinyItemAnalysis/server/DIF.R | 2059 ++++++++-- inst/shiny-examples/ShinyItemAnalysis/server/Data.R | 155 inst/shiny-examples/ShinyItemAnalysis/server/IRT.R | 28 inst/shiny-examples/ShinyItemAnalysis/server/Regression.R | 40 inst/shiny-examples/ShinyItemAnalysis/server/Summary.R | 3 inst/shiny-examples/ShinyItemAnalysis/server/TraditionalAnalysis.R | 36 inst/shiny-examples/ShinyItemAnalysis/titlepage.sty | 2 inst/shiny-examples/ShinyItemAnalysis/ui.R | 4 inst/shiny-examples/ShinyItemAnalysis/ui/uiAbout.R | 75 inst/shiny-examples/ShinyItemAnalysis/ui/uiDIF |only inst/shiny-examples/ShinyItemAnalysis/ui/uiDIF.R | 1480 +++---- inst/shiny-examples/ShinyItemAnalysis/ui/uiData.R | 724 +-- inst/shiny-examples/ShinyItemAnalysis/ui/uiReferences.R | 148 inst/shiny-examples/ShinyItemAnalysis/ui/uiRegression.R | 25 inst/shiny-examples/ShinyItemAnalysis/ui/uiReports.R | 69 inst/shiny-examples/ShinyItemAnalysis/ui/uiSetting.R | 5 inst/shiny-examples/ShinyItemAnalysis/ui/uiTraditionalAnalysis.R | 2 man/DDplot.Rd | 268 - man/DistractorAnalysis.Rd | 170 man/HCI.Rd | 63 man/HCIkey.Rd | 54 man/HCItest.Rd | 62 man/ItemAnalysis.Rd | 257 - man/LearningToLearn.Rd |only man/dataMedical.Rd | 89 man/dataMedicalgraded.Rd | 91 man/dataMedicalkey.Rd | 76 man/dataMedicaltest.Rd | 89 man/gDiscrim.Rd | 181 man/ggWrightMap.Rd | 128 man/plotAdjacent.Rd | 98 man/plotCumulative.Rd | 106 man/plotDIFLogistic.Rd | 150 man/plotDIFirt.Rd | 156 man/plotDistractorAnalysis.Rd | 203 man/plotMultinomial.Rd | 97 man/startShinyItemAnalysis.Rd | 54 man/theme_app.Rd | 71 83 files changed, 6827 insertions(+), 4404 deletions(-)
More information about ShinyItemAnalysis at CRAN
Permanent link
Title: Client for 'mapshaper' for 'Geospatial' Operations
Description: Edit and simplify 'geojson', 'Spatial', and 'sf'
objects. This is wrapper around the 'mapshaper' 'JavaScript' library
by Matthew Bloch <https://github.com/mbloch/mapshaper/> to perform
topologically-aware polygon simplification, as well as other
operations such as clipping, erasing, dissolving, and converting
'multi-part' to 'single-part' geometries. It relies on the
'geojsonio' package for working with 'geojson' objects, the 'sf'
package for working with 'sf' objects, and the 'sp' and 'rgdal'
packages for working with 'Spatial' objects.
Author: Andy Teucher [aut, cre],
Kenton Russell [aut] (JavaScript support),
Matthew Bloch [cph] (mapshaper Javascript library)
Maintainer: Andy Teucher <andy.teucher@gmail.com>
Diff between rmapshaper versions 0.4.2 dated 2020-01-17 and 0.4.3 dated 2020-01-28
DESCRIPTION | 47 ++++--- MD5 | 32 ++-- NEWS.md | 8 + R/clip_erase.R | 163 +++++++++++++------------ R/utils.R | 26 +++ R/zzz.R |only README.md | 13 + inst/doc/rmapshaper.R | 2 inst/doc/rmapshaper.Rmd | 4 inst/doc/rmapshaper.html | 52 ++----- man/ms_clip.Rd | 73 +++++------ man/ms_erase.Rd | 80 ++++++------ tests/testthat/helper-tests.R | 7 + tests/testthat/test-apply_mapshaper_commands.R |only tests/testthat/test-clip_erase.R | 21 +++ tests/testthat/test-utils.R | 4 tools/readme/unnamed-chunk-4-1.png |binary vignettes/rmapshaper.Rmd | 4 18 files changed, 303 insertions(+), 233 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 0.4.3 dated 2020-01-24 and 0.4.4 dated 2020-01-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ build/rlang.pdf |binary tests/testthat/test-deparse.R | 1 + 5 files changed, 13 insertions(+), 7 deletions(-)
Title: Fill Missing Values in Vectors
Description: Edit vectors to fill missing values, based on the vector itself.
Author: Jelger van Zaane [aut, cre]
Maintainer: Jelger van Zaane <me@jelgervanzaane.nl>
Diff between fillr versions 0.1.1 dated 2019-08-02 and 1.0.0 dated 2020-01-28
DESCRIPTION | 17 +++--- MD5 | 44 ++++++++------- NAMESPACE | 3 - NEWS.md | 8 ++ R/fill_missing.R | 5 + R/fill_missing_interval.R |only R/fill_vector.R | 45 +++++++++++++++ README.md | 79 +++++++++++++++++++++++----- inst |only man/check_some_missing.Rd | 36 ++++++------ man/fill_missing.Rd | 40 +++++++------- man/fill_missing_interval.Rd |only man/fill_missing_last.Rd | 50 ++++++++--------- man/fill_missing_max.Rd | 50 ++++++++--------- man/fill_missing_min.Rd | 50 ++++++++--------- man/fill_missing_previous.Rd | 50 ++++++++--------- man/fill_missing_strict.Rd | 50 ++++++++--------- man/fill_value.Rd | 42 +++++++------- man/fill_vector_interval.Rd |only man/fill_vector_last.Rd | 30 +++++----- man/fill_vector_max.Rd | 30 +++++----- man/fill_vector_min.Rd | 30 +++++----- man/fill_vector_previous.Rd | 26 ++++----- man/fill_vector_strict.Rd | 30 +++++----- tests/spelling.R |only tests/testthat/test-fill_missing_interval.R |only 26 files changed, 416 insertions(+), 299 deletions(-)
Title: Spatial Graph-Theoretic Genetic Gravity Modelling
Description: Implementation of spatial graph-theoretic genetic gravity models.
The model framework is applicable for other types of spatial flow questions.
Includes functions for constructing spatial graphs, sampling and summarizing
associated raster variables and building unconstrained and singly constrained
gravity models.
Author: Jeffrey S. Evans [aut, cre],
Melanie Murphy [aut]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between GeNetIt versions 0.1-2 dated 2019-10-03 and 0.1-3 dated 2020-01-28
DESCRIPTION | 10 +- MD5 | 48 +++++----- NAMESPACE | 2 R/compare.models.R | 30 +++--- R/knn.graph.R | 2 R/node.statistics.R |only inst/CITATION | 4 inst/NEWS | 5 + man/area.graph.statistics.Rd | 38 ++++---- man/build.node.data.Rd | 88 +++++++++--------- man/compare.models.Rd | 87 +++++++++--------- man/dmatrix.df.Rd | 80 ++++++++--------- man/dps.Rd | 24 ++--- man/flow.Rd | 84 +++++++++--------- man/graph.statistics.Rd | 163 ++++++++++++++++++----------------- man/gravity.Rd | 200 +++++++++++++++++++++---------------------- man/gravity.es.Rd | 88 +++++++++--------- man/knn.graph.Rd | 141 +++++++++++++++--------------- man/node.statistics.Rd |only man/plot.gravity.Rd | 68 +++++++------- man/predict.gravity.Rd | 42 ++++----- man/print.gravity.Rd | 30 +++--- man/ralu.model.Rd | 68 +++++++------- man/ralu.site.Rd | 64 ++++++------- man/rasters.Rd | 50 +++++----- man/summary.gravity.Rd | 36 +++---- 26 files changed, 741 insertions(+), 711 deletions(-)
Title: Inference of Gene Regulatory Networks
Description: We present 'corto' (Correlation Tool), a simple package to infer
gene regulatory networks and visualize master regulators from gene expression
data using DPI (Data Processing Inequality) and bootstrapping to recover edges.
An initial step is performed to calculate all significant
edges between a list of source nodes (centroids) and target genes.
Then all triplets containing two centroids and one target are tested
in a DPI step which removes edges. A bootstrapping
process then calculates the robustness of the network, eventually re-adding
edges previously removed by DPI. The package implements a similar pipeline as
ARACNe-AP (Algorithm for the Reconstruction of Accurate Cellular Networks with
Adaptive Partitioning) by Giorgi (2016) <doi:10.1093/bioinformatics/btw216>)
with optimizations to run outside a computing cluster (most notably
correlation to infer feature dependencies instead of Mutual Information).
Author: Federico M. Giorgi [aut, cre],
Daniele Mercatelli [ctb],
Gonzalo Lopez-Garcia [ctb]
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>
Diff between corto versions 0.99.10 dated 2019-10-30 and 1.0.1 dated 2020-01-28
DESCRIPTION | 18 - MD5 | 56 +-- NAMESPACE | 44 +- R/corto.R | 6 R/functions.R | 48 ++ R/gsea.R | 2 R/mra.R |only README.md | 29 + inst/CITATION | 4 inst/doc/corto_vignette.R | 24 - inst/doc/corto_vignette.Rmd | 11 inst/doc/corto_vignette.html | 724 ++++++++++++++++++++++++------------------- man/corto.Rd | 117 +++--- man/fcor.Rd | 44 +- man/fisherp.Rd | 40 +- man/gsea.Rd | 88 ++--- man/gsea2.Rd | 99 +++-- man/kmgformat.Rd | 70 ++-- man/mra.Rd |only man/mraplot.Rd |only man/p2r.Rd | 42 +- man/p2z.Rd | 42 +- man/plot_gsea.Rd | 95 +++-- man/plot_gsea2.Rd | 81 ++-- man/r2p.Rd | 42 +- man/scatter.Rd |only man/slice.Rd | 42 +- man/stouffer.Rd | 42 +- man/wstouffer.Rd | 48 +- man/z2p.Rd | 40 +- vignettes/corto_vignette.Rmd | 11 31 files changed, 1059 insertions(+), 850 deletions(-)
Title: Calculate MIMS Dissolved Gas Concentrations Without Getting a
Headache
Description: Calculate dissolved gas concentrations from raw MIMS
(Membrane Inlet Mass Spectrometer) signal data. Use mimsy() on
a formatted CSV file to return dissolved gas concentrations
(mg and microMole) of N2, O2, Ar based on
gas solubility at temperature, pressure, and salinity. See references
Benson and Krause (1984) <DOI:10.4319/lo.1992.37.6.1307>, Garcia and
Gordon (1992) <DOI:10.4319/lo.1984.29.3.0620>, Stull (1947)
<DOI:10.1021/ie50448a022>, and Hamme and Emerson (2004)
<DOI:10.1016/j.dsr.2004.06.009> for more information. Easily save the
output to a nicely-formatted multi-tab 'Excel' workbook with mimsy.save().
Supports dual-temperature standard calibration for dual-bath MIMS setups.
Author: Michelle C. Kelly [aut, cre]
Maintainer: Michelle C. Kelly <michellecatherinekelly@gmail.com>
Diff between mimsy versions 0.4.2 dated 2019-03-10 and 0.4.3 dated 2020-01-28
DESCRIPTION | 16 LICENSE | 2 MD5 | 32 - NAMESPACE | 22 NEWS.md | 98 ++-- R/mimsy.R | 1146 +++++++++++++++++++++++++------------------------- R/mimsy.save.R | 86 +-- README.md | 123 ++--- build/vignette.rds |binary inst/doc/mimsy.R | 129 ++--- inst/doc/mimsy.Rmd | 302 ++++++------- inst/doc/mimsy.html | 767 +++++++++++++++++++++------------ inst/extdata/data.csv | 86 +-- man/mimsy.Rd | 131 +++-- man/mimsy.save.Rd | 58 +- vignettes/data.csv | 86 +-- vignettes/mimsy.Rmd | 302 ++++++------- 17 files changed, 1787 insertions(+), 1599 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-21 1.1.3
2015-04-30 1.1.2
2014-11-26 1.1.1
2014-08-15 1.0.1
2014-07-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-22 1.0.15
2019-08-26 1.0.14
2018-06-14 1.0.13
2018-03-10 1.0.12
2018-01-14 1.0.11
2017-12-15 1.0.10
2017-11-30 1.0.9
2017-10-07 1.0.8
2017-09-15 1.0.7
2017-08-16 1.0.6
2017-06-21 1.0.5
2017-05-13 1.0.4
2017-04-16 1.0.3
2017-02-23 1.0.2
2017-01-29 1.0.1
2016-12-29 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-19 1.5.3
2017-07-20 1.5.2
2017-04-10 1.5.1
2017-03-12 1.5
2016-12-20 1.4.1
2016-04-12 1.3-1
2015-04-25 1.3
2013-12-23 1.2.1
2012-07-06 1.2
2012-04-23 1.1
2012-04-20 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-01 0.1.3
2018-12-14 0.1.2
2018-12-02 0.1.1
2018-10-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-16 0.9.7
2016-10-17 0.9.6
2016-08-04 0.9.5
2016-07-22 0.9.2
2016-07-14 0.9.1
2016-06-13 0.9.0
2016-05-30 0.6.2
2016-05-18 0.5.1
2016-02-09 0.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-23 0.4.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-12 0.0-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-08 0.2
2019-01-11 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-19 0.9.7
2017-08-28 0.9.6
2016-12-21 0.9.5
2016-12-14 0.9.4
2016-09-22 0.9.3
2016-07-15 0.9.2
2016-06-16 0.9.1
2016-03-28 0.9.0
2015-12-15 0.5
Title: Penalized Quantile Regression
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions including group penalties. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
Author: Ben Sherwood [aut, cre], Adam Maidman [ctb]
Maintainer: Ben Sherwood <ben.sherwood@ku.edu>
Diff between rqPen versions 2.2 dated 2019-12-10 and 2.2.1 dated 2020-01-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 5 +++++ R/mainFunctions.R | 4 ++-- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Interface to the 'Orcid.org' API
Description: Client for the 'Orcid.org' API (<https://orcid.org/>).
Functions included for searching for people, searching by 'DOI',
and searching by 'Orcid' 'ID'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rorcid versions 0.5.0 dated 2019-06-07 and 0.6.0 dated 2020-01-28
DESCRIPTION | 13 +- LICENSE | 2 MD5 | 104 +++++++++++------- NEWS.md | 29 +++++ R/orcid_citations.R | 85 ++++++++------ R/orcid_search.R | 88 +++++++++------ R/zzz.R | 84 +++++++++++++- README.md | 196 ++++++++++++++-------------------- build/vignette.rds |binary data/issn_title.rda |binary inst/ignore/issn_title_collect.R | 15 ++ man/orcid.Rd | 34 ++++- man/orcid_auth.Rd | 9 + man/orcid_citations.Rd | 14 +- man/orcid_distinctions.Rd | 9 + man/orcid_doi.Rd | 3 man/orcid_educations.Rd | 9 + man/orcid_employments.Rd | 9 + man/orcid_external_identifiers.Rd | 8 + man/orcid_fundings.Rd | 9 + man/orcid_invited_positions.Rd | 9 + man/orcid_keywords.Rd | 3 man/orcid_memberships.Rd | 9 + man/orcid_other_names.Rd | 3 man/orcid_peer_reviews.Rd | 9 + man/orcid_qualifications.Rd | 9 + man/orcid_research_resources.Rd | 9 + man/orcid_researcher_urls.Rd | 3 man/orcid_search.Rd | 53 +++++++-- man/orcid_services.Rd | 9 + man/rorcid-package.Rd | 8 - tests/fixtures |only tests/testthat/helper-rorcid.R |only tests/testthat/test-as.orcid.R | 18 +-- tests/testthat/test-extract_bibtex.R |only tests/testthat/test-identifiers.R | 46 ++++--- tests/testthat/test-orcid.R | 38 +++--- tests/testthat/test-orcid_citations.R |only tests/testthat/test-orcid_doi.R | 16 +- tests/testthat/test-orcid_id.R | 28 +++- tests/testthat/test-orcid_search.R |only tests/testthat/test-works.R | 21 ++- 42 files changed, 651 insertions(+), 360 deletions(-)
Title: 'Foreach' Parallel Adapter Using the 'Redis' Database
Description: A parallel back end for the 'foreach' package using the 'Redis'
database.
Author: B. W. Lewis <blewis@illposed.net>
Maintainer: B. W. Lewis <blewis@illposed.net>
Diff between doRedis versions 1.1.1 dated 2014-04-03 and 2.0.0 dated 2020-01-28
doRedis-1.1.1/doRedis/COPYING |only doRedis-1.1.1/doRedis/R/task.R |only doRedis-1.1.1/doRedis/README |only doRedis-1.1.1/doRedis/inst/ec2-redis-worker-installer.sh |only doRedis-1.1.1/doRedis/inst/redis-worker-installer.sh |only doRedis-1.1.1/doRedis/man/doRedis-internal.Rd |only doRedis-1.1.1/doRedis/man/setGetTask.Rd |only doRedis-1.1.1/doRedis/man/setTag.Rd |only doRedis-1.1.1/doRedis/man/setTaskLabel.Rd |only doRedis-2.0.0/doRedis/DESCRIPTION | 21 doRedis-2.0.0/doRedis/MD5 | 77 - doRedis-2.0.0/doRedis/NAMESPACE | 48 doRedis-2.0.0/doRedis/R/doRedis.R | 850 +++++++++--- doRedis-2.0.0/doRedis/R/package.R |only doRedis-2.0.0/doRedis/R/redisWorker.R | 403 +++-- doRedis-2.0.0/doRedis/R/redux.R |only doRedis-2.0.0/doRedis/README.md |only doRedis-2.0.0/doRedis/build/vignette.rds |binary doRedis-2.0.0/doRedis/inst/doc/Amazon.Rnw |only doRedis-2.0.0/doRedis/inst/doc/Amazon.pdf |only doRedis-2.0.0/doRedis/inst/doc/Debug.R |only doRedis-2.0.0/doRedis/inst/doc/Debug.Rnw |only doRedis-2.0.0/doRedis/inst/doc/Debug.pdf |only doRedis-2.0.0/doRedis/inst/doc/Service.Rnw |only doRedis-2.0.0/doRedis/inst/doc/Service.pdf |only doRedis-2.0.0/doRedis/inst/doc/doRedis.R |only doRedis-2.0.0/doRedis/inst/doc/doRedis.Rnw | 1032 ++++++--------- doRedis-2.0.0/doRedis/inst/doc/doRedis.pdf |binary doRedis-2.0.0/doRedis/inst/scripts |only doRedis-2.0.0/doRedis/man/doRedis-package.Rd | 62 doRedis-2.0.0/doRedis/man/dot-doRedis.Rd |only doRedis-2.0.0/doRedis/man/jobs.Rd |only doRedis-2.0.0/doRedis/man/logger.Rd |only doRedis-2.0.0/doRedis/man/redisConnect.Rd |only doRedis-2.0.0/doRedis/man/redisDelete.Rd |only doRedis-2.0.0/doRedis/man/redisGet.Rd |only doRedis-2.0.0/doRedis/man/redisSet.Rd |only doRedis-2.0.0/doRedis/man/redisWorker.Rd | 115 - doRedis-2.0.0/doRedis/man/registerDoRedis.Rd | 97 - doRedis-2.0.0/doRedis/man/removeJob.Rd |only doRedis-2.0.0/doRedis/man/removeQueue.Rd | 54 doRedis-2.0.0/doRedis/man/setChunkSize.Rd | 48 doRedis-2.0.0/doRedis/man/setExport.Rd | 33 doRedis-2.0.0/doRedis/man/setFtinterval.Rd |only doRedis-2.0.0/doRedis/man/setPackages.Rd |only doRedis-2.0.0/doRedis/man/setProgress.Rd |only doRedis-2.0.0/doRedis/man/setReduce.Rd |only doRedis-2.0.0/doRedis/man/startLocalWorkers.Rd | 109 - doRedis-2.0.0/doRedis/man/tasks.Rd |only doRedis-2.0.0/doRedis/src/Makevars.win | 4 doRedis-2.0.0/doRedis/src/alive.c | 307 +++- doRedis-2.0.0/doRedis/tests |only doRedis-2.0.0/doRedis/vignettes/Amazon.Rnw |only doRedis-2.0.0/doRedis/vignettes/Debug.Rnw |only doRedis-2.0.0/doRedis/vignettes/Service.Rnw |only doRedis-2.0.0/doRedis/vignettes/doRedis.Rnw | 1032 ++++++--------- doRedis-2.0.0/doRedis/vignettes/elastic.jpg |only doRedis-2.0.0/doRedis/vignettes/keys.jpg |binary doRedis-2.0.0/doRedis/vignettes/textpos.sty |only 59 files changed, 2295 insertions(+), 1997 deletions(-)
Title: Flexible Genotyping for Polyploids
Description: Implements empirical Bayes approaches to genotype
polyploids from next generation sequencing data while
accounting for allelic bias, overdispersion, and sequencing
error. The main functions are flexdog() and multidog(),
which allow the specification
of many different genotype distributions. An experimental
function that takes into account varying levels of relatedness
is implemented in mupdog(). Also provided are functions to
simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as
functions to calculate oracle genotyping error rates, oracle_mis(), and
correlation with the true genotypes, oracle_cor(). These latter two
functions are useful for read depth calculations. Run
browseVignettes(package = "updog") in R for example usage. See
Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and
Gerard and Ferrao (2019) <doi:10.1093/bioinformatics/btz852> for details
on the implemented methods.
Author: David Gerard [aut, cre] (<https://orcid.org/0000-0001-9450-5023>)
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between updog versions 1.1.3 dated 2019-11-21 and 1.2.0 dated 2020-01-28
updog-1.1.3/updog/inst/doc/parallel_computing.R |only updog-1.1.3/updog/inst/doc/parallel_computing.Rmd |only updog-1.1.3/updog/inst/doc/parallel_computing.html |only updog-1.1.3/updog/vignettes/parallel_computing.Rmd |only updog-1.2.0/updog/DESCRIPTION | 15 updog-1.2.0/updog/MD5 | 65 - updog-1.2.0/updog/NAMESPACE | 4 updog-1.2.0/updog/NEWS.md | 151 ++-- updog-1.2.0/updog/R/ashdog.R | 41 - updog-1.2.0/updog/R/multidog.R |only updog-1.2.0/updog/R/plot_mupdog.R | 581 +++++++-------- updog-1.2.0/updog/R/updog.R | 293 +++---- updog-1.2.0/updog/R/vem.R | 10 updog-1.2.0/updog/README.md | 20 updog-1.2.0/updog/build/vignette.rds |binary updog-1.2.0/updog/inst/doc/multidog.R |only updog-1.2.0/updog/inst/doc/multidog.Rmd |only updog-1.2.0/updog/inst/doc/multidog.html |only updog-1.2.0/updog/inst/doc/oracle_calculations.Rmd | 271 +++---- updog-1.2.0/updog/inst/doc/oracle_calculations.html | 590 ++++++--------- updog-1.2.0/updog/inst/doc/simulate_ngs.Rmd | 5 updog-1.2.0/updog/inst/doc/simulate_ngs.html | 742 ++++++++------------ updog-1.2.0/updog/inst/doc/smells_like_updog.Rmd | 201 ++--- updog-1.2.0/updog/inst/doc/smells_like_updog.html | 637 +++++++---------- updog-1.2.0/updog/man/flexdog.Rd | 2 updog-1.2.0/updog/man/flexdog_full.Rd | 10 updog-1.2.0/updog/man/format_multidog.Rd |only updog-1.2.0/updog/man/is.multidog.Rd |only updog-1.2.0/updog/man/multidog.Rd |only updog-1.2.0/updog/man/mupdog.Rd | 6 updog-1.2.0/updog/man/plot.multidog.Rd |only updog-1.2.0/updog/man/updog-package.Rd | 3 updog-1.2.0/updog/src/em.cpp | 2 updog-1.2.0/updog/src/flexdog.cpp | 5 updog-1.2.0/updog/src/weighted_em_const.cpp | 16 updog-1.2.0/updog/tests/testthat/test_cvxr.R | 112 +-- updog-1.2.0/updog/vignettes/multidog.Rmd |only updog-1.2.0/updog/vignettes/oracle_calculations.Rmd | 271 +++---- updog-1.2.0/updog/vignettes/simulate_ngs.Rmd | 5 updog-1.2.0/updog/vignettes/smells_like_updog.Rmd | 201 ++--- 40 files changed, 1963 insertions(+), 2296 deletions(-)
Title: Create Full Text Browsers from Annotated Token Lists
Description: Create browsers for reading full texts from a token list format.
Information obtained from text analyses (e.g., topic modeling, word scaling)
can be used to annotate the texts.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between tokenbrowser versions 0.1.1 dated 2019-10-24 and 0.1.2 dated 2020-01-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/html_misc.r | 4 +++- R/wrap_documents.r | 2 -- tests/testthat/test_tokenvis.r | 3 ++- 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Comparison of Phylogenetic Trees Using Quartet and Split
Measures
Description: Calculates the number of four-taxon subtrees consistent with a pair
of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986),
Reconstructing the shape of a tree from observed dissimilarity data,
Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>,
and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for
computing the quartet and triplet distances between binary or general trees,
Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157>
for pairs of binary trees.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Andreas Sand [ant],
Gerth Stølting Brodal [ant],
Rolf Fagerberg [ant],
Thomas Mailund [ant],
Christian N. S. Pedersen [ant],
Jens Johansen [ant],
Morten K. Holt [ant]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Quartet versions 1.0.3 dated 2019-12-30 and 1.1.0 dated 2020-01-28
Quartet-1.0.3/Quartet/R/ReleaseQuestions.R |only Quartet-1.0.3/Quartet/R/TreeManipulation.R |only Quartet-1.0.3/Quartet/man/StatusToMatrix.Rd |only Quartet-1.0.3/Quartet/man/UnshiftTree.Rd |only Quartet-1.0.3/Quartet/src/Quartet-init.c |only Quartet-1.0.3/Quartet/tests/trees |only Quartet-1.1.0/Quartet/DESCRIPTION | 15 Quartet-1.1.0/Quartet/MD5 | 152 +++-- Quartet-1.1.0/Quartet/NAMESPACE | 33 + Quartet-1.1.0/Quartet/NEWS.md | 9 Quartet-1.1.0/Quartet/R/Metrics.R | 228 +++++--- Quartet-1.1.0/Quartet/R/PartitionDistance.R | 127 ++-- Quartet-1.1.0/Quartet/R/QuartetDistance.R | 139 +++-- Quartet-1.1.0/Quartet/R/RcppExports.R | 191 ++++--- Quartet-1.1.0/Quartet/R/ResolvedQuartets.R | 6 Quartet-1.1.0/Quartet/R/TernaryPoints.R | 8 Quartet-1.1.0/Quartet/R/tqDist.r | 259 ++++++---- Quartet-1.1.0/Quartet/R/zzz.R |only Quartet-1.1.0/Quartet/build/partial.rdb |binary Quartet-1.1.0/Quartet/inst/CITATION | 43 + Quartet-1.1.0/Quartet/inst/WORDLIST |only Quartet-1.1.0/Quartet/inst/doc/Critical-distances.R | 13 Quartet-1.1.0/Quartet/inst/doc/Critical-distances.Rmd | 20 Quartet-1.1.0/Quartet/inst/doc/Critical-distances.pdf |binary Quartet-1.1.0/Quartet/inst/doc/Tree-distance-metrics.Rmd | 12 Quartet-1.1.0/Quartet/inst/doc/Tree-distance-metrics.pdf |binary Quartet-1.1.0/Quartet/inst/trees |only Quartet-1.1.0/Quartet/man/AllQuartets.Rd | 3 Quartet-1.1.0/Quartet/man/CompareQuartets.Rd | 6 Quartet-1.1.0/Quartet/man/CompareSplits.Rd | 37 - Quartet-1.1.0/Quartet/man/Distances.Rd | 4 Quartet-1.1.0/Quartet/man/PairSharedQuartetStatus.Rd | 3 Quartet-1.1.0/Quartet/man/PairSharedSplitStatus.Rd | 16 Quartet-1.1.0/Quartet/man/PlotQuartet.Rd | 3 Quartet-1.1.0/Quartet/man/QuartetPoints.Rd | 7 Quartet-1.1.0/Quartet/man/QuartetState.Rd | 55 +- Quartet-1.1.0/Quartet/man/QuartetStatus.Rd | 61 ++ Quartet-1.1.0/Quartet/man/ResolvedQuartets.Rd | 3 Quartet-1.1.0/Quartet/man/SimilarityMetrics.Rd | 79 +-- Quartet-1.1.0/Quartet/man/SplitStatus.Rd | 7 Quartet-1.1.0/Quartet/man/SymmetricDifferenceLineEnds.Rd | 3 Quartet-1.1.0/Quartet/man/TQDist.Rd | 38 - Quartet-1.1.0/Quartet/man/TQFile.Rd | 3 Quartet-1.1.0/Quartet/man/ValidateQuartetFile.Rd | 3 Quartet-1.1.0/Quartet/man/dot-AddSlice.Rd |only Quartet-1.1.0/Quartet/man/dot-NormalizeStatus.Rd |only Quartet-1.1.0/Quartet/man/dot-StatusToMatrix.Rd |only Quartet-1.1.0/Quartet/man/tqdist_QuartetDistance.Rd | 44 + Quartet-1.1.0/Quartet/src/EdgeParser.cpp |only Quartet-1.1.0/Quartet/src/NewickParser.cpp | 46 + Quartet-1.1.0/Quartet/src/QuartetDistanceCalculator.cpp | 223 ++++++++ Quartet-1.1.0/Quartet/src/QuartetDistanceCalculator.h | 31 + Quartet-1.1.0/Quartet/src/RcppExports.cpp | 118 ++++ Quartet-1.1.0/Quartet/src/RootedTree.cpp | 4 Quartet-1.1.0/Quartet/src/edge_parser.h |only Quartet-1.1.0/Quartet/src/hdt.h | 7 Quartet-1.1.0/Quartet/src/newick_parser.h | 3 Quartet-1.1.0/Quartet/src/rQuartetDist.cpp | 161 ++++++ Quartet-1.1.0/Quartet/src/unrooted_tree.h | 13 Quartet-1.1.0/Quartet/tests/figs |only Quartet-1.1.0/Quartet/tests/testthat/test-1-tqdist.R | 75 +- Quartet-1.1.0/Quartet/tests/testthat/test-PartitionDistance.R | 28 - Quartet-1.1.0/Quartet/tests/testthat/test-QuartetDistance.R | 55 +- Quartet-1.1.0/Quartet/tests/testthat/test-ResolvedQuartets.R | 6 Quartet-1.1.0/Quartet/tests/testthat/test-ZZZ-Metrics.R | 39 - Quartet-1.1.0/Quartet/vignettes/Critical-distances.Rmd | 20 Quartet-1.1.0/Quartet/vignettes/Tree-distance-metrics.Rmd | 12 67 files changed, 1696 insertions(+), 775 deletions(-)
Title: Ridge Estimation of Vector Auto-Regressive (VAR) Processes
Description: The ragt2ridges-package provides ridge maximum likelihood estimation of vector auto-regressive processes: the VAR(1), VAR(2) and VARX(1) model (more to be added). Prior knowledge may be incorporated in the estimation through a) specification of the edges believed to be absent in the time series chain graph, and b) a shrinkage target towards which the parameter estimate is shrunken for large penalty parameter values. Estimation functionality is accompanied by methodology for penalty parameter selection. In addition, the package offers supporting functionality for the exploitation of estimated models. Among others, i) a procedure to infer the support of the non-sparse ridge estimate (and thereby of the time series chain graph) is implemented, ii) a table of node-wise network summary statistics, iii) mutual information analysis, and iv) impulse response analysis. Cf. Miok et al. (2017) <DOI:10.1002/bimj.201500269> and Miok et al. (2019) <DOI:10.1002/bimj.201700195> for details on the implemented methods.
Author: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between ragt2ridges versions 0.3.3 dated 2019-12-05 and 0.3.4 dated 2020-01-28
DESCRIPTION | 11 +++++------ MD5 | 4 ++-- inst/NEWS.Rd | 6 ++++++ 3 files changed, 13 insertions(+), 8 deletions(-)
Title: Tropical Fisheries Analysis
Description: A compilation of fish stock assessment methods for the
analysis of length-frequency data in the context of data-poor
fisheries. Includes methods and examples included in the FAO
Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish
stock assessment"
(<http://www.fao.org/documents/card/en/c/9bb12a06-2f05-5dcb-a6ca-2d6dd3080f65/>),
as well as other more recent methods.
Author: Tobias K. Mildenberger, Marc H. Taylor, Matthias Wolff
Maintainer: Tobias K. Mildenberger <t.k.mildenberger@gmail.com>
Diff between TropFishR versions 1.6.1 dated 2019-01-17 and 1.6.2 dated 2020-01-28
TropFishR-1.6.1/TropFishR/inst/doc/TropFishR.bib |only TropFishR-1.6.1/TropFishR/inst/doc/news.html |only TropFishR-1.6.1/TropFishR/inst/doc/news.md |only TropFishR-1.6.2/TropFishR/DESCRIPTION | 14 TropFishR-1.6.2/TropFishR/MD5 | 95 - TropFishR-1.6.2/TropFishR/R/Bhattacharya.R | 2 TropFishR-1.6.2/TropFishR/R/ELEFAN.R | 35 TropFishR-1.6.2/TropFishR/R/ELEFAN_GA.R | 316 ++-- TropFishR-1.6.2/TropFishR/R/ELEFAN_SA.R | 38 TropFishR-1.6.2/TropFishR/R/VPA.R | 21 TropFishR-1.6.2/TropFishR/R/Z_BevertonHolt.R | 6 TropFishR-1.6.2/TropFishR/R/catchCurve.R | 33 TropFishR-1.6.2/TropFishR/R/lfqCreate.R | 6 TropFishR-1.6.2/TropFishR/R/lfqModify.R | 285 +-- TropFishR-1.6.2/TropFishR/R/plot.catchCurve.R | 19 TropFishR-1.6.2/TropFishR/R/powell_wetherall.R | 282 +-- TropFishR-1.6.2/TropFishR/R/recruitment.R | 2 TropFishR-1.6.2/TropFishR/R/select.R | 2 TropFishR-1.6.2/TropFishR/README.md | 14 TropFishR-1.6.2/TropFishR/build/vignette.rds |binary TropFishR-1.6.2/TropFishR/inst/doc/Using_TropFishR_ELEFAN_functions.R | 94 - TropFishR-1.6.2/TropFishR/inst/doc/Using_TropFishR_ELEFAN_functions.Rmd | 99 - TropFishR-1.6.2/TropFishR/inst/doc/Using_TropFishR_ELEFAN_functions.html | 738 ++++++--- TropFishR-1.6.2/TropFishR/inst/doc/lfqData.R | 10 TropFishR-1.6.2/TropFishR/inst/doc/lfqData.html | 426 ++++- TropFishR-1.6.2/TropFishR/inst/doc/tutorial.R | 24 TropFishR-1.6.2/TropFishR/inst/doc/tutorial.html | 759 ++++++---- TropFishR-1.6.2/TropFishR/man/ELEFAN.Rd | 38 TropFishR-1.6.2/TropFishR/man/ELEFAN_GA.Rd | 30 TropFishR-1.6.2/TropFishR/man/ELEFAN_SA.Rd | 25 TropFishR-1.6.2/TropFishR/man/M_empirical.Rd | 18 TropFishR-1.6.2/TropFishR/man/VPA.Rd | 15 TropFishR-1.6.2/TropFishR/man/catchCurve.Rd | 13 TropFishR-1.6.2/TropFishR/man/gillnetfit.Rd | 10 TropFishR-1.6.2/TropFishR/man/growth_length_age.Rd | 16 TropFishR-1.6.2/TropFishR/man/lfqCreate.Rd | 18 TropFishR-1.6.2/TropFishR/man/lfqFitCurves.Rd | 14 TropFishR-1.6.2/TropFishR/man/lfqModify.Rd | 17 TropFishR-1.6.2/TropFishR/man/plot.VPA.Rd | 18 TropFishR-1.6.2/TropFishR/man/plot.catchCurve.Rd | 15 TropFishR-1.6.2/TropFishR/man/plot.lfq.Rd | 29 TropFishR-1.6.2/TropFishR/man/plot.predict_mod.Rd | 20 TropFishR-1.6.2/TropFishR/man/plot.recruitment.Rd | 10 TropFishR-1.6.2/TropFishR/man/plot.select.Rd | 3 TropFishR-1.6.2/TropFishR/man/plot.select_Millar.Rd | 19 TropFishR-1.6.2/TropFishR/man/powell_wetherall.Rd | 9 TropFishR-1.6.2/TropFishR/man/predict_mod.Rd | 25 TropFishR-1.6.2/TropFishR/man/prod_mod_ts.Rd | 10 TropFishR-1.6.2/TropFishR/man/select_Millar.Rd | 9 TropFishR-1.6.2/TropFishR/vignettes/Using_TropFishR_ELEFAN_functions.Rmd | 99 - 50 files changed, 2309 insertions(+), 1491 deletions(-)
Title: Rank-Based Tests for General Factorial Designs
Description: The rankFD() function calculates the Wald-type statistic (WTS) and the ANOVA-type
statistic (ATS) for nonparametric factorial designs, e.g., for count, ordinal or score data
in a crossed design with an arbitrary number of factors.
Author: Frank Konietschke, Sarah Friedrich, Edgar Brunner, Markus Pauly
Maintainer: Frank Konietschke <frank.konietschke@charite.de>
Diff between rankFD versions 0.0.4 dated 2020-01-27 and 0.0.5 dated 2020-01-28
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ranktwosamples.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Psychometric Modeling Infrastructure
Description: Infrastructure for psychometric modeling such as data classes (for
item response data and paired comparisons), basic model fitting functions (for
Bradley-Terry, Rasch, parametric logistic IRT, generalized partial credit,
rating scale, multinomial processing tree models), extractor functions for
different types of parameters (item, person, threshold, discrimination,
guessing, upper asymptotes), unified inference and visualizations, and various
datasets for illustration. Intended as a common lightweight and efficient
toolbox for psychometric modeling and a common building block for fitting
psychometric mixture models in package "psychomix" and trees based on
psychometric models in package "psychotree".
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>),
Carolin Strobl [aut],
Florian Wickelmaier [aut],
Basil Komboz [aut],
Julia Kopf [aut],
Lennart Schneider [aut],
Rudolf Debelak [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between psychotools versions 0.5-0 dated 2018-12-19 and 0.5-1 dated 2020-01-28
DESCRIPTION | 8 - MD5 | 44 +++--- NEWS | 6 build/partial.rdb |binary data/ConspiracistBeliefs2016.rda |binary data/FirstNames.rda |binary data/GermanParties2009.rda |binary data/MathExam14W.rda |binary data/MemoryDeficits.rda |binary data/PairClustering.rda |binary data/Sim3PL.rda |binary data/SoundQuality.rda |binary data/SourceMonitoring.rda |binary data/StereotypeThreat.rda |binary data/VerbalAggression.rda |binary data/YouthGratitude.rda |binary man/VerbalAggression.Rd | 5 man/curveplot.Rd | 2 man/personpar.Rd | 2 man/piplot.Rd | 2 man/profileplot.Rd | 2 man/raschmodel.Rd | 2 tests/Examples/psychotools-Ex.Rout.save | 220 +++++++++++++------------------- 23 files changed, 138 insertions(+), 155 deletions(-)
Title: Process Digital Images of a Vegetation Cover
Description: A collection of functions to process digital images, depict greenness index trajectories and extract relevant phenological stages.
Author: Gianluca Filippa, Edoardo Cremonese, Mirco Migliavacca, Marta Galvagno, Matthias Folker, Andrew D. Richardson, Enrico Tomelleri
Maintainer: Gianluca Filippa <gian.filippa@gmail.com>
Diff between phenopix versions 2.3.1 dated 2017-06-16 and 2.4 dated 2020-01-28
phenopix-2.3.1/phenopix/R/DrawROI.R |only phenopix-2.3.1/phenopix/man/DrawROI.Rd |only phenopix-2.4/phenopix/DESCRIPTION | 13 - phenopix-2.4/phenopix/MD5 | 50 +++---- phenopix-2.4/phenopix/NAMESPACE | 9 - phenopix-2.4/phenopix/R/DrawMULTIROI.R |only phenopix-2.4/phenopix/R/PrintROI.R | 30 +--- phenopix-2.4/phenopix/R/convertROI.R |only phenopix-2.4/phenopix/R/extractParameters.R | 2 phenopix-2.4/phenopix/R/extractVIs.R | 120 ++++++++++-------- phenopix-2.4/phenopix/R/getExposure.R | 18 ++ phenopix-2.4/phenopix/R/greenClusters.R | 3 phenopix-2.4/phenopix/R/plotSpatial.R | 17 +- phenopix-2.4/phenopix/R/splitROI.R | 8 - phenopix-2.4/phenopix/R/updateROI.R | 30 +--- phenopix-2.4/phenopix/data/bartlett2009.filtered.rda |binary phenopix-2.4/phenopix/data/bartlett2009.fitted.rda |binary phenopix-2.4/phenopix/data/bartlett2009.processed.rda |binary phenopix-2.4/phenopix/data/bartlett2009.rda |binary phenopix-2.4/phenopix/man/BeckFit.Rd | 2 phenopix-2.4/phenopix/man/CutSeason.Rd | 13 + phenopix-2.4/phenopix/man/DrawMULTIROI.Rd |only phenopix-2.4/phenopix/man/convert.Rd | 6 phenopix-2.4/phenopix/man/convertROI.Rd |only phenopix-2.4/phenopix/man/editExposure.Rd | 6 phenopix-2.4/phenopix/man/extractVIs.Rd | 7 - phenopix-2.4/phenopix/man/getExposure.Rd | 8 + phenopix-2.4/phenopix/man/phenopix-package.Rd | 22 ++- phenopix-2.4/phenopix/man/plotSum.Rd | 6 29 files changed, 209 insertions(+), 161 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects from statistical models and returns the
result as tidy data frames. These data frames are ready to use with the
'ggplot2'-package. Marginal effects can be calculated for many different
models. Interaction terms, splines and polynomial terms are also supported.
The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a
generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between ggeffects versions 0.14.0 dated 2019-12-16 and 0.14.1 dated 2020-01-28
ggeffects-0.14.0/ggeffects/R/reshape_helpers.R |only ggeffects-0.14.0/ggeffects/R/select_helpers.R |only ggeffects-0.14.0/ggeffects/man/reexports.Rd |only ggeffects-0.14.0/ggeffects/tests/testthat/test-glmRob.R |only ggeffects-0.14.1/ggeffects/DESCRIPTION | 23 - ggeffects-0.14.1/ggeffects/MD5 | 158 ++++---- ggeffects-0.14.1/ggeffects/NAMESPACE | 22 - ggeffects-0.14.1/ggeffects/NEWS.md | 15 ggeffects-0.14.1/ggeffects/R/emmeans_prediction_data.R | 20 - ggeffects-0.14.1/ggeffects/R/get_predictions_cgam.R |only ggeffects-0.14.1/ggeffects/R/get_predictions_clm.R | 13 ggeffects-0.14.1/ggeffects/R/get_predictions_clm2.R | 15 ggeffects-0.14.1/ggeffects/R/get_predictions_clmm.R | 21 - ggeffects-0.14.1/ggeffects/R/get_predictions_generic.R | 1 ggeffects-0.14.1/ggeffects/R/get_predictions_lm.R | 4 ggeffects-0.14.1/ggeffects/R/get_predictions_mixor.R |only ggeffects-0.14.1/ggeffects/R/get_predictions_multinom.R | 2 ggeffects-0.14.1/ggeffects/R/get_predictions_polr.R | 2 ggeffects-0.14.1/ggeffects/R/get_predictions_stan.R | 28 - ggeffects-0.14.1/ggeffects/R/get_predictions_survival.R | 4 ggeffects-0.14.1/ggeffects/R/get_predictions_vglm.R | 8 ggeffects-0.14.1/ggeffects/R/getter.R | 3 ggeffects-0.14.1/ggeffects/R/ggeffect.R | 9 ggeffects-0.14.1/ggeffects/R/ggemmeans.R | 3 ggeffects-0.14.1/ggeffects/R/ggemmeans_add_confint.R | 53 +- ggeffects-0.14.1/ggeffects/R/ggpredict.R | 32 - ggeffects-0.14.1/ggeffects/R/plot.R | 14 ggeffects-0.14.1/ggeffects/R/post_processing_predictions.R | 4 ggeffects-0.14.1/ggeffects/R/predict_zero_inflation.R | 8 ggeffects-0.14.1/ggeffects/R/predictions.R | 5 ggeffects-0.14.1/ggeffects/R/print.R | 43 -- ggeffects-0.14.1/ggeffects/R/standard_error_predictions.R | 96 ----- ggeffects-0.14.1/ggeffects/R/utils.R | 8 ggeffects-0.14.1/ggeffects/R/utils_get_data_grid.R | 9 ggeffects-0.14.1/ggeffects/R/utils_get_representative_values.R | 10 ggeffects-0.14.1/ggeffects/R/utils_handle_labels.R | 23 + ggeffects-0.14.1/ggeffects/R/utils_is_empty.R | 42 +- ggeffects-0.14.1/ggeffects/R/utils_model_function.R | 2 ggeffects-0.14.1/ggeffects/R/utils_reshape.R |only ggeffects-0.14.1/ggeffects/R/utils_select.R |only ggeffects-0.14.1/ggeffects/R/utils_typical_value.R | 182 +++++----- ggeffects-0.14.1/ggeffects/R/vcov.R | 54 ++ ggeffects-0.14.1/ggeffects/README.md | 60 ++- ggeffects-0.14.1/ggeffects/build/partial.rdb |binary ggeffects-0.14.1/ggeffects/build/vignette.rds |binary ggeffects-0.14.1/ggeffects/inst/doc/ggeffects.R | 14 ggeffects-0.14.1/ggeffects/inst/doc/ggeffects.Rmd | 16 ggeffects-0.14.1/ggeffects/inst/doc/ggeffects.html | 14 ggeffects-0.14.1/ggeffects/inst/doc/introduction_effectsatvalues.R | 7 ggeffects-0.14.1/ggeffects/inst/doc/introduction_effectsatvalues.Rmd | 7 ggeffects-0.14.1/ggeffects/inst/doc/introduction_effectsatvalues.html | 14 ggeffects-0.14.1/ggeffects/inst/doc/introduction_plotcustomize.R | 3 ggeffects-0.14.1/ggeffects/inst/doc/introduction_plotcustomize.Rmd | 3 ggeffects-0.14.1/ggeffects/inst/doc/introduction_plotcustomize.html | 12 ggeffects-0.14.1/ggeffects/inst/doc/introduction_plotmethod.R | 49 +- ggeffects-0.14.1/ggeffects/inst/doc/introduction_plotmethod.Rmd | 49 +- ggeffects-0.14.1/ggeffects/inst/doc/introduction_plotmethod.html | 57 +-- ggeffects-0.14.1/ggeffects/inst/doc/introduction_randomeffects.R | 6 ggeffects-0.14.1/ggeffects/inst/doc/introduction_randomeffects.Rmd | 6 ggeffects-0.14.1/ggeffects/inst/doc/introduction_randomeffects.html | 58 +-- ggeffects-0.14.1/ggeffects/inst/doc/practical_logisticmixedmodel.R | 7 ggeffects-0.14.1/ggeffects/inst/doc/practical_logisticmixedmodel.Rmd | 7 ggeffects-0.14.1/ggeffects/inst/doc/practical_logisticmixedmodel.html | 43 +- ggeffects-0.14.1/ggeffects/inst/doc/practical_robustestimation.R |only ggeffects-0.14.1/ggeffects/inst/doc/practical_robustestimation.Rmd |only ggeffects-0.14.1/ggeffects/inst/doc/practical_robustestimation.html |only ggeffects-0.14.1/ggeffects/inst/doc/technical_differencepredictemmeans.R | 5 ggeffects-0.14.1/ggeffects/inst/doc/technical_differencepredictemmeans.Rmd | 5 ggeffects-0.14.1/ggeffects/inst/doc/technical_differencepredictemmeans.html | 95 ++--- ggeffects-0.14.1/ggeffects/inst/doc/technical_stata.R | 4 ggeffects-0.14.1/ggeffects/inst/doc/technical_stata.Rmd | 4 ggeffects-0.14.1/ggeffects/inst/doc/technical_stata.html | 39 +- ggeffects-0.14.1/ggeffects/man/get_title.Rd | 3 ggeffects-0.14.1/ggeffects/man/ggpredict.Rd | 29 - ggeffects-0.14.1/ggeffects/man/vcov.Rd | 15 ggeffects-0.14.1/ggeffects/tests/testthat/test-lmer.R | 7 ggeffects-0.14.1/ggeffects/tests/testthat/test-negbin.R | 9 ggeffects-0.14.1/ggeffects/vignettes/ggeffects.Rmd | 16 ggeffects-0.14.1/ggeffects/vignettes/introduction_effectsatvalues.Rmd | 7 ggeffects-0.14.1/ggeffects/vignettes/introduction_plotcustomize.Rmd | 3 ggeffects-0.14.1/ggeffects/vignettes/introduction_plotmethod.Rmd | 49 +- ggeffects-0.14.1/ggeffects/vignettes/introduction_randomeffects.Rmd | 6 ggeffects-0.14.1/ggeffects/vignettes/practical_logisticmixedmodel.Rmd | 7 ggeffects-0.14.1/ggeffects/vignettes/practical_robustestimation.Rmd |only ggeffects-0.14.1/ggeffects/vignettes/technical_differencepredictemmeans.Rmd | 5 ggeffects-0.14.1/ggeffects/vignettes/technical_stata.Rmd | 4 86 files changed, 873 insertions(+), 807 deletions(-)
Title: Oceanographic Data Sets for 'oce' Package
Description: Several Oceanographic data sets are provided for use
by the 'oce' package and for other purposes.
Author: Dan Kelley [aut, cre] (<https://orcid.org/0000-0001-7808-5911>)
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>
Diff between ocedata versions 0.1.5 dated 2018-12-19 and 0.1.6 dated 2020-01-28
ocedata-0.1.5/ocedata/data/coastlineWorldFine.rda |only ocedata-0.1.5/ocedata/data/coastlineWorldMedium.rda |only ocedata-0.1.5/ocedata/data/datalist |only ocedata-0.1.5/ocedata/data/geosecs235.rda |only ocedata-0.1.6/ocedata/DESCRIPTION | 17 ++--- ocedata-0.1.6/ocedata/MD5 | 33 ++++++---- ocedata-0.1.6/ocedata/NAMESPACE | 5 - ocedata-0.1.6/ocedata/NEWS | 4 + ocedata-0.1.6/ocedata/R |only ocedata-0.1.6/ocedata/README.md | 16 +++- ocedata-0.1.6/ocedata/data/coastlineWorldFine.R |only ocedata-0.1.6/ocedata/data/coastlineWorldMedium.R |only ocedata-0.1.6/ocedata/data/geosecs235.R |only ocedata-0.1.6/ocedata/inst/WORDLIST |only ocedata-0.1.6/ocedata/inst/extdata/coastlineWorldFine_slots.rda |only ocedata-0.1.6/ocedata/inst/extdata/coastlineWorldMedium_slots.rda |only ocedata-0.1.6/ocedata/inst/extdata/geosecs235_slots.rda |only ocedata-0.1.6/ocedata/man/coastlineWorldMedium.Rd | 2 ocedata-0.1.6/ocedata/man/geosecs235.Rd | 2 ocedata-0.1.6/ocedata/man/levitus.Rd | 2 ocedata-0.1.6/ocedata/man/oce-class.Rd |only ocedata-0.1.6/ocedata/man/riley.Rd | 2 ocedata-0.1.6/ocedata/man/topo2.Rd | 4 - ocedata-0.1.6/ocedata/tests/testthat/test_geosecs235.R |only ocedata-0.1.6/ocedata/tests/testthat/test_presenttime.R |only 25 files changed, 52 insertions(+), 35 deletions(-)
Title: Calculate Total Points and Probabilities for Nomogram
Description: A nomogram, which can be carried out in 'rms' package, provides a
graphical explanation of a prediction process. However, it is not very easy
to draw straight lines, read points and probabilities accurately. Even, it
is hard for users to calculate total points and probabilities for all
subjects.
This package provides formula_rd() and formula_lp() functions to fit the
formula of total points with raw data and linear predictors respectively by
polynomial regression. Function points_cal() will help you calculate the
total points. prob_cal() can be used to calculate the probabilities after
lrm(), cph() or psm() regression.
For more complex condition, interaction or restricted cubic spine, TotalPoints.rms()
can be used.
Author: Jing Zhang, Zhi Jin
Maintainer: Jing Zhang<zj391120@163.com>
Diff between nomogramFormula versions 1.1.0.0 dated 2019-09-02 and 1.2.0.0 dated 2020-01-28
DESCRIPTION | 12 +++++++----- MD5 | 10 ++++++---- NAMESPACE | 1 + R/TotalPoints.rms.R |only R/prob_cal.R | 37 +++++++++++++++++++++++++++++++------ man/TotalPoints.rms.Rd |only man/prob_cal.Rd | 9 ++++++++- 7 files changed, 53 insertions(+), 16 deletions(-)
More information about nomogramFormula at CRAN
Permanent link
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and
writing data between R and other statistical software packages like 'SPSS',
'SAS' or 'Stata', and working with labelled data. This includes easy ways
to get, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
David Ranzolin [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.1.2 dated 2020-01-17 and 1.1.3 dated 2020-01-28
DESCRIPTION | 6 - MD5 | 14 +-- NEWS.md | 6 + R/tidy_labels.R | 2 inst/doc/intro_sjlabelled.html | 175 ++++++++++++++++++++--------------------- inst/doc/labelleddata.html | 12 +- inst/doc/quasiquotation.html | 153 ++++++++++++++++++----------------- man/tidy_labels.Rd | 2 8 files changed, 191 insertions(+), 179 deletions(-)
Title: Serializable Representations
Description: String and binary representations of objects for several formats /
mime types.
Author: Philipp Angerer [aut, cre] (<https://orcid.org/0000-0002-0369-2888>),
Thomas Kluyver [aut],
Jan Schulz [aut],
abielr [ctb],
Denilson Figueiredo de Sa [ctb],
Jim Hester [ctb],
karldw [ctb],
Dave Foster [ctb],
Carson Sievert [ctb]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between repr versions 1.0.2 dated 2019-12-16 and 1.1.0 dated 2020-01-28
DESCRIPTION | 8 +- MD5 | 30 ++++----- R/options.r | 8 +- R/repr_matrix_df.r | 31 +++------ R/repr_vector.r | 61 +++++++++++++----- R/utils.r | 15 ++++ man/repr-options.Rd | 5 + man/repr_-times-.function.Rd | 8 -- man/repr_-times-.matrix-slash-data.frame.Rd | 64 +++++++++++++------ man/repr_-times-.recordedplot.Rd | 28 ++++++-- man/repr_-times-.ts.Rd | 3 man/repr_-times-.vector.Rd | 38 ++++++----- tests/testthat/helpers.r | 5 - tests/testthat/test_array_manipulation.r | 57 ++++++++--------- tests/testthat/test_escaping.r | 39 ++++++------ tests/testthat/test_repr_vector.r | 90 ++++++++++++++++------------ 16 files changed, 287 insertions(+), 203 deletions(-)
Title: Utility Functions for Large-scale Data
Description: Utility functions for large-scale data. For now, package 'bigutilsr'
mainly includes functions for outlier detection and PCA projection.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigutilsr versions 0.2.2 dated 2019-11-04 and 0.3.0 dated 2020-01-28
bigutilsr-0.2.2/bigutilsr/man/to_maha.Rd |only bigutilsr-0.3.0/bigutilsr/DESCRIPTION | 16 bigutilsr-0.3.0/bigutilsr/MD5 | 74 +- bigutilsr-0.3.0/bigutilsr/NAMESPACE | 62 +- bigutilsr-0.3.0/bigutilsr/R/KNN.R | 48 - bigutilsr-0.3.0/bigutilsr/R/OGK.R |only bigutilsr-0.3.0/bigutilsr/R/RcppExports.R | 30 - bigutilsr-0.3.0/bigutilsr/R/bigutilsr-package.R | 11 bigutilsr-0.3.0/bigutilsr/R/outlier-dist.R | 297 ++++------ bigutilsr-0.3.0/bigutilsr/R/outlier-hist.R | 256 ++++---- bigutilsr-0.3.0/bigutilsr/R/outlier-tukey.R | 98 +-- bigutilsr-0.3.0/bigutilsr/R/pca-project.R | 160 ++--- bigutilsr-0.3.0/bigutilsr/R/procrustes.R | 192 +++--- bigutilsr-0.3.0/bigutilsr/R/reexports.R | 36 - bigutilsr-0.3.0/bigutilsr/R/rollmean.R | 52 - bigutilsr-0.3.0/bigutilsr/R/utils.R |only bigutilsr-0.3.0/bigutilsr/README.md | 36 - bigutilsr-0.3.0/bigutilsr/inst/WORDLIST | 4 bigutilsr-0.3.0/bigutilsr/man/LOF.Rd | 14 bigutilsr-0.3.0/bigutilsr/man/as_model_matrix.Rd |only bigutilsr-0.3.0/bigutilsr/man/covRob.Rd |only bigutilsr-0.3.0/bigutilsr/man/covrob_ogk.Rd |only bigutilsr-0.3.0/bigutilsr/man/hist_out.Rd | 2 bigutilsr-0.3.0/bigutilsr/man/knn_parallel.Rd | 18 bigutilsr-0.3.0/bigutilsr/man/maha_trans.Rd |only bigutilsr-0.3.0/bigutilsr/man/predict.Procrustes.Rd | 2 bigutilsr-0.3.0/bigutilsr/man/prob_dist.Rd | 4 bigutilsr-0.3.0/bigutilsr/man/procrustes.Rd | 8 bigutilsr-0.3.0/bigutilsr/man/reexports.Rd | 5 bigutilsr-0.3.0/bigutilsr/man/rollmean.Rd | 2 bigutilsr-0.3.0/bigutilsr/man/tukey_mc_up.Rd | 4 bigutilsr-0.3.0/bigutilsr/src/RcppExports.cpp | 24 bigutilsr-0.3.0/bigutilsr/src/ogk.cpp |only bigutilsr-0.3.0/bigutilsr/tests/spelling.R | 6 bigutilsr-0.3.0/bigutilsr/tests/testthat.R | 8 bigutilsr-0.3.0/bigutilsr/tests/testthat/test-OGK.R |only bigutilsr-0.3.0/bigutilsr/tests/testthat/test-knn.R | 66 +- bigutilsr-0.3.0/bigutilsr/tests/testthat/test-lof.R | 88 +- bigutilsr-0.3.0/bigutilsr/tests/testthat/test-outlier-hist.R | 98 +-- bigutilsr-0.3.0/bigutilsr/tests/testthat/test-outlier-tukey.R | 40 - bigutilsr-0.3.0/bigutilsr/tests/testthat/test-pca-project.R | 154 ++--- bigutilsr-0.3.0/bigutilsr/tests/testthat/test-rollmean.R | 32 - bigutilsr-0.3.0/bigutilsr/tests/testthat/test-utils.R |only 43 files changed, 1005 insertions(+), 942 deletions(-)
Title: PARAFAC Analysis of EEMs from DOM
Description: This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.
Author: Matthias Pucher [aut, cre],
Daniel Graeber [aut, ctb],
Stefan Preiner [ctb],
Renata Pinto [ctb]
Maintainer: Matthias Pucher <matthias.pucher@wcl.ac.at>
Diff between staRdom versions 1.1.1 dated 2019-11-27 and 1.1.3 dated 2020-01-28
DESCRIPTION | 10 ++--- MD5 | 20 +++++----- R/eem_importers.R | 14 ++++++- R/parafac_plot_functions.R | 36 +++++++++++++++---- R/plot_functions.R | 18 +++++++-- README | 8 ++++ build/vignette.rds |binary inst/EEM_simple_analysis.Rmd | 22 +++++------ inst/doc/Basic_analysis_of_DOM_samples.html | 12 +++--- inst/doc/PARAFAC_analysis_of_EEM.html | 52 ++++++++++++++-------------- man/eem_overview_plot.Rd | 7 ++- 11 files changed, 124 insertions(+), 75 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to
encode spatial vector data. Binds to 'GDAL' for reading and writing
data, to 'GEOS' for geometrical operations, and to 'PROJ' for
projection conversions and datum transformations.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Kirill M<U+00FC>ller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.8-0 dated 2019-09-17 and 0.8-1 dated 2020-01-28
sf-0.8-0/sf/tests/testthat/Rplots.pdf |only sf-0.8-0/sf/tests/zzz.R |only sf-0.8-0/sf/tests/zzz.Rout.save |only sf-0.8-1/sf/DESCRIPTION | 33 +- sf-0.8-1/sf/MD5 | 207 +++++++------- sf-0.8-1/sf/NAMESPACE | 65 ++++ sf-0.8-1/sf/NEWS.md | 34 ++ sf-0.8-1/sf/R/RcppExports.R | 56 ++- sf-0.8-1/sf/R/cast_sfc.R | 20 + sf-0.8-1/sf/R/cast_sfg.R | 16 - sf-0.8-1/sf/R/crs.R | 32 +- sf-0.8-1/sf/R/db.R | 9 sf-0.8-1/sf/R/gdal_utils.R | 81 ++++- sf-0.8-1/sf/R/geom.R | 105 ------- sf-0.8-1/sf/R/grid.R | 2 sf-0.8-1/sf/R/join.R | 20 + sf-0.8-1/sf/R/m_range.R |only sf-0.8-1/sf/R/make_grid.R |only sf-0.8-1/sf/R/maps.R | 84 +++++ sf-0.8-1/sf/R/read.R | 26 + sf-0.8-1/sf/R/sample.R | 140 +++++---- sf-0.8-1/sf/R/sf.R | 14 sf-0.8-1/sf/R/sfc.R | 30 +- sf-0.8-1/sf/R/shift_longitude.R |only sf-0.8-1/sf/R/spatstat.R | 259 ++++++++++++++++-- sf-0.8-1/sf/R/stars.R | 4 sf-0.8-1/sf/R/tidyverse-vctrs.R |only sf-0.8-1/sf/R/tidyverse.R | 19 - sf-0.8-1/sf/R/transform.R | 18 - sf-0.8-1/sf/R/wkt.R | 17 - sf-0.8-1/sf/R/z_range.R |only sf-0.8-1/sf/build/vignette.rds |binary sf-0.8-1/sf/demo/twitter.R | 9 sf-0.8-1/sf/inst/doc/sf1.R | 98 +++--- sf-0.8-1/sf/inst/doc/sf1.html | 76 ++--- sf-0.8-1/sf/inst/doc/sf2.R | 42 +- sf-0.8-1/sf/inst/doc/sf2.html | 29 +- sf-0.8-1/sf/inst/doc/sf3.R | 62 ++-- sf-0.8-1/sf/inst/doc/sf3.html | 12 sf-0.8-1/sf/inst/doc/sf4.R | 28 - sf-0.8-1/sf/inst/doc/sf4.html | 78 ++--- sf-0.8-1/sf/inst/doc/sf5.R | 50 +-- sf-0.8-1/sf/inst/doc/sf5.html | 40 +- sf-0.8-1/sf/inst/doc/sf6.R | 18 - sf-0.8-1/sf/inst/doc/sf6.html | 26 - sf-0.8-1/sf/inst/docker/gdal/Dockerfile | 22 - sf-0.8-1/sf/inst/docker/lowest/Dockerfile | 82 +++-- sf-0.8-1/sf/man/aggregate.sf.Rd | 11 sf-0.8-1/sf/man/coerce-methods.Rd | 8 sf-0.8-1/sf/man/dbDataType.Rd | 1 sf-0.8-1/sf/man/gdal.Rd | 54 ++- sf-0.8-1/sf/man/gdal_utils.Rd | 51 +++ sf-0.8-1/sf/man/geos_measures.Rd | 11 sf-0.8-1/sf/man/geos_unary.Rd | 10 sf-0.8-1/sf/man/plot.Rd | 148 ++++++++-- sf-0.8-1/sf/man/sf-deprecated.Rd | 11 sf-0.8-1/sf/man/sf.Rd | 14 sf-0.8-1/sf/man/sf_project.Rd | 6 sf-0.8-1/sf/man/st_as_binary.Rd | 22 + sf-0.8-1/sf/man/st_as_sf.Rd | 25 + sf-0.8-1/sf/man/st_as_sfc.Rd | 36 +- sf-0.8-1/sf/man/st_cast.Rd | 9 sf-0.8-1/sf/man/st_collection_extract.Rd | 28 + sf-0.8-1/sf/man/st_crs.Rd | 7 sf-0.8-1/sf/man/st_graticule.Rd | 13 sf-0.8-1/sf/man/st_join.Rd | 25 + sf-0.8-1/sf/man/st_m_range.Rd |only sf-0.8-1/sf/man/st_make_grid.Rd | 18 - sf-0.8-1/sf/man/st_read.Rd | 60 ++-- sf-0.8-1/sf/man/st_relate.Rd | 2 sf-0.8-1/sf/man/st_sample.Rd | 17 - sf-0.8-1/sf/man/st_shift_longitude.Rd |only sf-0.8-1/sf/man/st_transform.Rd | 12 sf-0.8-1/sf/man/st_write.Rd | 55 ++- sf-0.8-1/sf/man/st_z_range.Rd |only sf-0.8-1/sf/man/stars.Rd | 27 + sf-0.8-1/sf/man/tidyverse.Rd | 71 +++- sf-0.8-1/sf/man/vctrs.Rd |only sf-0.8-1/sf/src/RcppExports.cpp | 139 ++++++--- sf-0.8-1/sf/src/gdal.cpp | 10 sf-0.8-1/sf/src/gdal_read.cpp | 18 + sf-0.8-1/sf/src/gdal_utils.cpp | 135 +++++---- sf-0.8-1/sf/src/proj.cpp | 72 +++-- sf-0.8-1/sf/src/stars.cpp | 2 sf-0.8-1/sf/src/wkb.cpp | 6 sf-0.8-1/sf/src/zm_range.cpp |only sf-0.8-1/sf/src/zm_range.h |only sf-0.8-1/sf/tests/cast.R | 7 sf-0.8-1/sf/tests/cast.Rout.save | 34 +- sf-0.8-1/sf/tests/crs.R | 13 sf-0.8-1/sf/tests/crs.Rout.save | 14 sf-0.8-1/sf/tests/dplyr.R | 2 sf-0.8-1/sf/tests/dplyr.Rout.save | 6 sf-0.8-1/sf/tests/empty.Rout.save | 14 sf-0.8-1/sf/tests/geos.Rout.save | 8 sf-0.8-1/sf/tests/maps.R |only sf-0.8-1/sf/tests/maps.Rout.save |only sf-0.8-1/sf/tests/read.R | 8 sf-0.8-1/sf/tests/read.Rout.save | 16 + sf-0.8-1/sf/tests/sample.R |only sf-0.8-1/sf/tests/sample.Rout.save |only sf-0.8-1/sf/tests/sfc.R | 1 sf-0.8-1/sf/tests/sfc.Rout.save | 4 sf-0.8-1/sf/tests/sfg.Rout.save | 12 sf-0.8-1/sf/tests/spatstat.R |only sf-0.8-1/sf/tests/spatstat.Rout.save |only sf-0.8-1/sf/tests/testthat.Rout.save | 33 ++ sf-0.8-1/sf/tests/testthat/test-shift_longitude.R |only sf-0.8-1/sf/tests/testthat/test_deprecated-db.R | 2 sf-0.8-1/sf/tests/testthat/test_gdal.R | 5 sf-0.8-1/sf/tests/testthat/test_postgis_RPostgreSQL.R | 2 sf-0.8-1/sf/tests/testthat/test_postgis_RPostgres.R | 2 sf-0.8-1/sf/tests/testthat/test_sfg.R | 8 sf-0.8-1/sf/tests/testthat/test_vctrs.R |only sf-0.8-1/sf/tests/testthat/test_zm_range.R |only sf-0.8-1/sf/tests/wkb.Rout.save | 8 116 files changed, 2218 insertions(+), 1078 deletions(-)
Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Drabinova and Martinkova, 2017, doi:10.1111/jedm.12158).
Author: Adela Hladka [aut, cre],
Patricia Martinkova [aut],
Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>
Diff between difNLR versions 1.3.1 dated 2020-01-27 and 1.3.2 dated 2020-01-28
DESCRIPTION | 8 - MD5 | 52 +++--- NEWS.md | 9 + R/ddfMLR.R | 2 R/difNLR-package.R | 4 R/difNLR.R | 10 - R/difORD.R | 2 README.md | 2 man/GMAT.Rd | 96 ++++++------ man/GMAT2.Rd | 90 +++++------ man/GMAT2key.Rd | 74 ++++----- man/GMAT2test.Rd | 90 +++++------ man/GMATkey.Rd | 74 ++++----- man/GMATtest.Rd | 100 ++++++------ man/MSATB.Rd | 86 +++++------ man/MSATBkey.Rd | 72 ++++----- man/MSATBtest.Rd | 84 +++++----- man/NLR.Rd | 390 +++++++++++++++++++++++++------------------------- man/ORD.Rd | 262 ++++++++++++++++----------------- man/checkInterval.Rd | 74 ++++----- man/ddfMLR.Rd | 2 man/difNLR-package.Rd | 4 man/difNLR.Rd | 2 man/difORD.Rd | 2 man/estimNLR.Rd | 168 ++++++++++----------- man/formulaNLR.Rd | 200 ++++++++++++------------- man/startNLR.Rd | 222 ++++++++++++++-------------- 27 files changed, 1097 insertions(+), 1084 deletions(-)
Title: Co-Clustering Adjusted Rand Index and Bikm1 Procedure for
Contingency and Binary Data-Sets
Description: Co-clustering of the rows and columns of a contingency or binary matrix, or double binary matrices and model selection for the number of row and column clusters. Three models are considered: the Poisson latent block model for contingency matrix, the binary latent block model for binary matrix and a new model we develop: the multiple latent block model for double binary matrices. A new procedure named bikm1 is implemented to investigate more efficiently the grid of numbers of clusters. Then, the studied model selection criteria are the integrated completed likelihood (ICL) and the Bayesian integrated likelihood (BIC). Finally, the co-clustering adjusted Rand index (CARI) to measure agreement between co-clustering partitions is implemented. Robert Valerie and Vasseur Yann (2017) <arXiv:1705.06760>.
Author: Valerie Robert [aut, cre]
Maintainer: Valerie Robert <valerie.robert.math@gmail.com>
Diff between bikm1 versions 0.9.0 dated 2019-08-24 and 1.0.0 dated 2020-01-28
DESCRIPTION | 12 +- MD5 | 85 ++++++++--------- NEWS.md |only R/BIKM1_LBM_Binary-class.R | 79 +++++++++------- R/BIKM1_LBM_Poisson-class.R | 69 ++++++++------ R/BIKM1_MLBM_Binary-class.R | 89 +++++++++--------- R/bikm1-package.R | 10 +- R/bikm1_LBM_Binary_functions.R | 40 ++++---- R/bikm1_LBM_Poisson_functions.R | 28 ++--- R/bikm1_MLBM_Binary_functions.R | 154 ++++++++++++++++++++++---------- man/BIKM1_LBM_Binary-class.Rd | 16 +-- man/BIKM1_LBM_Binary-proc.Rd | 14 +- man/BIKM1_LBM_Poisson-class.Rd | 16 +-- man/BIKM1_LBM_Poisson-proc.Rd | 2 man/BIKM1_MLBM_Binary-class.Rd | 18 +-- man/BIKM1_MLBM_Binary-proc.Rd | 2 man/BinBlocICL_MLBM-proc.Rd | 2 man/BinBlocRnd_LBM-proc.Rd | 2 man/BinBlocRnd_MLBM-proc.Rd | 2 man/BinBlocVisuResum_LBM-proc.Rd | 4 man/BinBlocVisuResum_MLBM-proc.Rd | 2 man/BinBlocVisu_LBM-proc.Rd | 4 man/BinBlocVisu_MLBM-proc.Rd | 2 man/CARI-proc.Rd | 10 +- man/CE_LBM-proc.Rd | 10 +- man/CE_MLBM-proc.Rd | 8 - man/CE_simple-proc.Rd | 4 man/PoissonBlocBIC-proc.Rd | 4 man/PoissonBlocICL-proc.Rd | 2 man/PoissonBlocVisu-proc.Rd | 4 man/PoissonBlocVisuResum-proc.Rd | 2 man/bikm1-package.Rd | 10 +- man/plot-BIKM1_LBM_Binary-method.Rd | 7 - man/plot-BIKM1_LBM_Poisson-method.Rd | 3 man/plot-BIKM1_MLBM_Binary-method.Rd | 5 - man/print-BIKM1_LBM_Binary-method.Rd | 1 man/print-BIKM1_LBM_Poisson-method.Rd | 3 man/print-BIKM1_MLBM_Binary-method.Rd | 5 - man/show-BIKM1_LBM_Binary-method.Rd | 1 man/show-BIKM1_LBM_Poisson-method.Rd | 1 man/show-BIKM1_MLBM_Binary-method.Rd | 5 - man/summary-BIKM1_LBM_Binary-method.Rd | 1 man/summary-BIKM1_LBM_Poisson-method.Rd | 1 man/summary-BIKM1_MLBM_Binary-method.Rd | 5 - 44 files changed, 418 insertions(+), 326 deletions(-)
Title: Assertion and Message Functions
Description: Enhanced message functions (cat() / message() / warning() / error())
using wrappers around sprintf(). Also, multiple assertion functions
(e.g. to check class, length, values, files, arguments, etc.).
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigassertr versions 0.1.1 dated 2019-10-14 and 0.1.2 dated 2020-01-28
DESCRIPTION | 12 MD5 | 22 - NAMESPACE | 46 +-- R/assert.R | 532 +++++++++++++++++++++--------------------- R/bigassertr-package.R | 4 R/message.R | 66 ++--- README.md | 14 - man/bigassertr-package.Rd | 8 man/printf.Rd | 2 tests/testthat.R | 8 tests/testthat/test-assert.R | 322 ++++++++++++------------- tests/testthat/test-message.R | 24 - 12 files changed, 535 insertions(+), 525 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of 'MUMPS' (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis,
LU (or LDL^t) factorization and system solving.
Third part ordering libraries are included and can be used: 'PORD', 'METIS', 'SCOTCH'.
'MUMPS' method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194>
and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.
Author: Serguei Sokol [aut, cre],
Emmanuel Agullo [ctb],
Patrick Amestoy [ctb, cph],
Maurice Bremond [ctb],
Alfredo Buttari [ctb],
Philippe Combes [ctb],
Marie Durand [ctb],
Aurelia Fevre [ctb],
Abdou Guermouche [ctb],
Guillaume Joslin [ctb],
Jacko Koster [ctb],
Jean-Yves L'Excellent [ctb],
Stephane Pralet [ctb],
Chiara Puglisi [ctb],
Francois-Henry Rouet [ctb],
Wissam Sid-Lakhdar [ctb],
Tzvetomila Slavova [ctb],
Bora Ucar [ctb],
Clement Weisbecker [ctb],
Juergen Schulze [ctb],
George Karypis [ctb],
Douglas C. Schmidt [ctb],
Isamu Hasegawa [ctb],
Alexander Chemeris [ctb],
Makoto Matsumoto [ctb],
Takuji Nishimura [ctb],
Francois Pellegrini [ctb],
David Goudin [ctb],
Pascal Henon [ctb],
Pierre Ramet [ctb],
Sebastien Fourestier [ctb],
Jun-Ho Her [ctb],
Cedric Chevalier [ctb],
Timothy A. Davis [ctb, cph],
Iain S. Duff [ctb, cph],
John K. Reid [ctb, cph],
Richard Stallman [ctb],
Samuel Thibault [ctb, cph],
CERFACS [cph],
CNRS [cph],
ENS Lyon [cph],
INP Toulouse [cph],
INRIA [cph],
University of Bordeaux [cph],
Regents of the University of Minnesota [cph],
Free Software Foundation, Inc [cph],
Alexander Chemeris [cph],
Makoto Matsumoto [cph],
Takuji Nishimura [cph],
Universite de Bordeaux [cph],
CNRS [cph],
INRAE [cph]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.2.1-7 dated 2019-12-06 and 5.2.1-10 dated 2020-01-28
DESCRIPTION | 62 +++- MD5 | 115 ++++---- NEWS | 19 + inst/COPYRIGHTS | 2 man/rmumps-package.Rd | 2 src/lib/MUMPS_5.2.1/libseq/mpi.f | 17 + src/lib/MUMPS_5.2.1/src/ana_AMDMF.F | 4 src/lib/MUMPS_5.2.1/src/ana_orderings.F | 8 src/lib/MUMPS_5.2.1/src/dana_aux.F | 40 +- src/lib/MUMPS_5.2.1/src/dana_aux_par.F | 27 + src/lib/MUMPS_5.2.1/src/dana_driver.F | 3 src/lib/MUMPS_5.2.1/src/darrowheads.F | 4 src/lib/MUMPS_5.2.1/src/dfac_asm_master_ELT_m.F | 3 src/lib/MUMPS_5.2.1/src/dfac_asm_master_m.F | 7 src/lib/MUMPS_5.2.1/src/dfac_distrib_ELT.F | 5 src/lib/MUMPS_5.2.1/src/dfac_distrib_distentry.F | 5 src/lib/MUMPS_5.2.1/src/dfac_driver.F | 87 +++--- src/lib/MUMPS_5.2.1/src/dfac_front_LU_type1.F | 12 src/lib/MUMPS_5.2.1/src/dfac_front_LU_type2.F | 9 src/lib/MUMPS_5.2.1/src/dfac_front_aux.F | 11 src/lib/MUMPS_5.2.1/src/dfac_front_type2_aux.F | 14 - src/lib/MUMPS_5.2.1/src/dfac_lr.F | 56 ++-- src/lib/MUMPS_5.2.1/src/dfac_par_m.F | 3 src/lib/MUMPS_5.2.1/src/dfac_process_blfac_slave.F | 10 src/lib/MUMPS_5.2.1/src/dfac_process_blocfacto.F | 12 src/lib/MUMPS_5.2.1/src/dfac_process_blocfacto_LDLT.F | 14 - src/lib/MUMPS_5.2.1/src/dfac_process_contrib_type1.F | 10 src/lib/MUMPS_5.2.1/src/dfac_process_contrib_type2.F | 10 src/lib/MUMPS_5.2.1/src/dfac_process_contrib_type3.F | 11 src/lib/MUMPS_5.2.1/src/dfac_process_master2.F | 12 src/lib/MUMPS_5.2.1/src/dini_defaults.F | 9 src/lib/MUMPS_5.2.1/src/dlr_core.F | 20 - src/lib/MUMPS_5.2.1/src/dmumps_comm_buffer.F | 167 ++++++------ src/lib/MUMPS_5.2.1/src/dmumps_driver.F | 29 +- src/lib/MUMPS_5.2.1/src/dmumps_load.F | 11 src/lib/MUMPS_5.2.1/src/dmumps_ooc.F | 15 - src/lib/MUMPS_5.2.1/src/dmumps_save_restore.F | 15 - src/lib/MUMPS_5.2.1/src/dsol_aux.F | 6 src/lib/MUMPS_5.2.1/src/dsol_bwd_aux.F | 1 src/lib/MUMPS_5.2.1/src/dsol_c.F | 1 src/lib/MUMPS_5.2.1/src/dsol_driver.F | 124 ++++---- src/lib/MUMPS_5.2.1/src/dsol_fwd_aux.F | 1 src/lib/MUMPS_5.2.1/src/dsol_lr.F | 2 src/lib/MUMPS_5.2.1/src/fac_asm_build_sort_index_m.F | 2 src/lib/MUMPS_5.2.1/src/mpi_noop.h |only src/lib/MUMPS_5.2.1/src/mumps_io_thread.c | 2 src/lib/MUMPS_5.2.1/src/mumps_memory_mod.F | 26 + src/lib/MUMPS_5.2.1/src/mumps_static_mapping.F | 45 ++- src/lib/MUMPS_5.2.1/src/tools_common.F | 11 src/lib/scotch_6.0.4/src/Makefile.inc | 2 src/lib/scotch_6.0.4/src/Makefile.inc.macos | 2 src/lib/scotch_6.0.4/src/Makefile.inc.rmumps | 2 src/lib/scotch_6.0.4/src/Makefile.inc.win | 2 src/lib/scotch_6.0.4/src/libscotch/kgraph_band.c | 3 src/lib/scotch_6.0.4/src/libscotch/kgraph_map_fm.c | 12 src/lib/scotch_6.0.4/src/libscotch/library_graph_map_view.c | 2 src/lib/scotch_6.0.4/src/libscotch/mesh_io_habo.c | 6 src/lib/scotch_6.0.4/src/libscotch/wgraph_part_fm.c | 4 tests/testthat/test_rmumps.R | 2 59 files changed, 686 insertions(+), 432 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Implemented wing2015 for lassnags),
Bourdon Jean-François [ctb] (Implemented sensor_tracking)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 2.2.1 dated 2020-01-21 and 2.2.2 dated 2020-01-28
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 8 ++++++++ R/io_readLAS.r | 2 +- R/methods-LAS.r | 8 +++++--- inst/doc/lidR-computation-speed-LAScatalog.html | 2 +- src/LAS.cpp | 14 ++++++++++---- tests/testthat/Rplots.pdf |binary tests/testthat/test-LAS.R | 5 +++++ 9 files changed, 42 insertions(+), 21 deletions(-)
Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators (i.e.,
sandwich estimators) for ordinary and weighted least squares linear regression
models, including the bias-reduced linearization estimator introduced by Bell
and McCaffrey (2002)
<http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf> and
developed further by Pustejovsky and Tipton (2017)
<DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating
the variance- covariance matrix and for testing single- and multiple-
contrast hypotheses based on Wald test statistics. Tests of single regression
coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
contrast hypotheses use an approximation to Hotelling's T-squared distribution.
Methods are provided for a variety of fitted models, including lm() and mlm
objects, glm(), ivreg() (from package 'AER'), plm() (from package 'plm'), gls()
and lme() (from 'nlme'), lmer() (from `lme4`), robu() (from 'robumeta'), and
rma.uni() and rma.mv() (from 'metafor').
Author: James Pustejovsky [aut, cre] (<https://orcid.org/0000-0003-0591-9465>)
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.4.0 dated 2019-12-18 and 0.4.1 dated 2020-01-28
DESCRIPTION | 6 +-- MD5 | 20 ++++++------ NEWS | 4 ++ R/data-documentation.R | 55 +++++++++++++++++----------------- build/partial.rdb |binary inst/doc/meta-analysis-with-CRVE.Rmd | 6 +-- inst/doc/meta-analysis-with-CRVE.html | 10 +++--- inst/doc/panel-data-CRVE.html | 4 +- man/dropoutPrevention.Rd | 45 ++++++++++++++------------- tests/testthat/test_lmerMod.R | 16 ++++----- vignettes/meta-analysis-with-CRVE.Rmd | 6 +-- 11 files changed, 89 insertions(+), 83 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package helps
to design cartographic representations such as proportional symbols,
choropleth, typology, flows or discontinuities maps. It also offers several
features that improve the graphic presentation of maps, for instance, map
palettes, layout elements (scale, north arrow, title...), labels or legends.
See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>),
Nicolas Lambert [aut],
Ian Fellows [cph] (no overlap algorithm for labels, from wordcloud
package)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between cartography versions 2.2.1 dated 2019-09-27 and 2.3.0 dated 2020-01-28
cartography-2.2.1/cartography/man/carto.pal.info.Rd |only cartography-2.2.1/cartography/man/display.carto.all.Rd |only cartography-2.2.1/cartography/man/display.carto.pal.Rd |only cartography-2.2.1/cartography/man/getOuterBorders.Rd |only cartography-2.2.1/cartography/tests/testthat |only cartography-2.2.1/cartography/tests/testthat.R |only cartography-2.3.0/cartography/DESCRIPTION | 21 - cartography-2.3.0/cartography/MD5 | 186 +++++----- cartography-2.3.0/cartography/NAMESPACE | 1 cartography-2.3.0/cartography/NEWS.md | 20 + cartography-2.3.0/cartography/R/Package.R | 90 ++--- cartography-2.3.0/cartography/R/data.R | 26 + cartography-2.3.0/cartography/R/dotDensityLayer.R | 69 +--- cartography-2.3.0/cartography/R/getBorders.R | 4 cartography-2.3.0/cartography/R/getGridLayer.R | 1 cartography-2.3.0/cartography/R/getOuterBorders.R | 15 cartography-2.3.0/cartography/R/getTiles.R | 220 ++++++++++--- cartography-2.3.0/cartography/R/ghostLayer.R |only cartography-2.3.0/cartography/R/labelLayer.R | 14 cartography-2.3.0/cartography/R/palettes.R | 141 ++------ cartography-2.3.0/cartography/README.md | 1 cartography-2.3.0/cartography/build/vignette.rds |binary cartography-2.3.0/cartography/inst/doc/cartography.R | 24 - cartography-2.3.0/cartography/inst/doc/cartography.html | 20 - cartography-2.3.0/cartography/inst/tinytest |only cartography-2.3.0/cartography/man/barscale.Rd | 3 cartography-2.3.0/cartography/man/carto.pal.Rd | 71 ++-- cartography-2.3.0/cartography/man/cartography.Rd | 91 +++-- cartography-2.3.0/cartography/man/choroLayer.Rd | 35 +- cartography-2.3.0/cartography/man/coasts.spdf.Rd | 1 cartography-2.3.0/cartography/man/countries.spdf.Rd | 1 cartography-2.3.0/cartography/man/discLayer.Rd | 33 + cartography-2.3.0/cartography/man/dotDensityLayer.Rd | 40 +- cartography-2.3.0/cartography/man/frame.spdf.Rd | 1 cartography-2.3.0/cartography/man/getBorders.Rd | 32 + cartography-2.3.0/cartography/man/getBreaks.Rd | 3 cartography-2.3.0/cartography/man/getFigDim.Rd | 3 cartography-2.3.0/cartography/man/getGridData.Rd | 1 cartography-2.3.0/cartography/man/getLinkLayer.Rd | 14 cartography-2.3.0/cartography/man/getTiles.Rd | 19 - cartography-2.3.0/cartography/man/ghostLayer.Rd |only cartography-2.3.0/cartography/man/gradLinkLayer.Rd | 28 + cartography-2.3.0/cartography/man/gradLinkTypoLayer.Rd | 38 +- cartography-2.3.0/cartography/man/graticule.spdf.Rd | 1 cartography-2.3.0/cartography/man/labelLayer.Rd | 19 - cartography-2.3.0/cartography/man/layoutLayer.Rd | 24 + cartography-2.3.0/cartography/man/legendBarsSymbols.Rd | 21 - cartography-2.3.0/cartography/man/legendChoro.Rd | 22 + cartography-2.3.0/cartography/man/legendCirclesSymbols.Rd | 19 - cartography-2.3.0/cartography/man/legendGradLines.Rd | 15 cartography-2.3.0/cartography/man/legendPropLines.Rd | 15 cartography-2.3.0/cartography/man/legendPropTriangles.Rd | 22 + cartography-2.3.0/cartography/man/legendSquaresSymbols.Rd | 21 - cartography-2.3.0/cartography/man/legendTypo.Rd | 18 - cartography-2.3.0/cartography/man/nuts0.df.Rd | 4 cartography-2.3.0/cartography/man/nuts0.spdf.Rd | 1 cartography-2.3.0/cartography/man/nuts1.df.Rd | 4 cartography-2.3.0/cartography/man/nuts1.spdf.Rd | 1 cartography-2.3.0/cartography/man/nuts2.df.Rd | 4 cartography-2.3.0/cartography/man/nuts2.spdf.Rd | 1 cartography-2.3.0/cartography/man/nuts3.df.Rd | 4 cartography-2.3.0/cartography/man/nuts3.spdf.Rd | 1 cartography-2.3.0/cartography/man/propLinkLayer.Rd | 27 + cartography-2.3.0/cartography/man/propSymbolsChoroLayer.Rd | 48 ++ cartography-2.3.0/cartography/man/propSymbolsLayer.Rd | 32 + cartography-2.3.0/cartography/man/propSymbolsTypoLayer.Rd | 41 +- cartography-2.3.0/cartography/man/propTrianglesLayer.Rd | 29 + cartography-2.3.0/cartography/man/smoothLayer.Rd | 35 +- cartography-2.3.0/cartography/man/twincities.df.Rd | 1 cartography-2.3.0/cartography/man/typoLayer.Rd | 26 + cartography-2.3.0/cartography/man/world.spdf.Rd | 1 cartography-2.3.0/cartography/tests/tinytest.R |only 72 files changed, 1102 insertions(+), 622 deletions(-)
Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space
Models
Description: Efficient methods for Bayesian inference of state space models
via particle Markov chain Monte Carlo and parallel importance sampling type weighted
Markov chain Monte Carlo (Vihola, Helske, and Franks, 2017, <arXiv:1609.02541>).
Gaussian, Poisson, binomial, or negative binomial
observation densities and basic stochastic volatility models with Gaussian state
dynamics, as well as general non-linear Gaussian models and discretised diffusion models
are supported.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>),
Matti Vihola [aut] (<https://orcid.org/0000-0002-8041-7222>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between bssm versions 0.1.8-1 dated 2020-01-07 and 0.1.9 dated 2020-01-28
DESCRIPTION | 8 ++-- MD5 | 18 ++++----- NAMESPACE | 1 NEWS | 6 +++ R/print_mcmc.R | 86 ++++++++++++++++++++------------------------- R/run_mcmc.R | 6 +++ inst/doc/bssm.html | 10 ++--- inst/doc/growth_model.html | 4 +- src/R_mcmc.cpp | 1 src/mcmc.cpp | 9 ++-- 10 files changed, 78 insertions(+), 71 deletions(-)
Title: Fast Bayesian Inference in Large Gaussian Graphical Models
Description: Fast Bayesian inference of marginal and conditional independence structures from high-dimensional data.
Author: Gwenael G.R. Leday [cre, aut],
Ilaria Speranza [aut],
Harry Gray [ctb]
Maintainer: Gwenael G.R. Leday <gwenael.leday@mrc-bsu.cam.ac.uk>
Diff between beam versions 2.0.0 dated 2020-01-26 and 2.0.1 dated 2020-01-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 3 +++ src/beam.cpp | 11 ++++++++--- 4 files changed, 17 insertions(+), 9 deletions(-)
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions
used in 'mlr3' and its companion packages. Comes with helper functions
for functional programming, for printing, to work with 'data.table',
as well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3misc versions 0.1.6 dated 2019-12-12 and 0.1.7 dated 2020-01-28
DESCRIPTION | 24 ++++++++++++-------- MD5 | 33 +++++++++++++++------------- NAMESPACE | 1 NEWS.md | 9 +++++++ R/cite_bib.R | 11 +++++---- R/encapsulate.R | 11 +++++++-- R/printf.R | 43 ++++++++++++++++++++++++++++++------- R/purrr_map.R | 14 ++++++------ R/with_package.R |only README.md | 7 +++++- man/cite_bib.Rd | 21 ++++++++++-------- man/compat-map.Rd | 9 +++++-- man/encapsulate.Rd | 11 +++++++-- man/mlr3misc-package.Rd | 5 ++++ man/printf.Rd | 23 ++++++++++++++++--- man/with_package.Rd |only tests/testthat/test_encapsulate.R | 4 +++ tests/testthat/test_map.R | 6 +++++ tests/testthat/test_with_package.R |only 19 files changed, 168 insertions(+), 64 deletions(-)
Title: Fingertips Data for Public Health
Description: Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Author: Sebastian Fox [aut, cre],
Julian Flowers [aut, ctb],
Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>),
Duncan Gormansway [ctb],
Carl Ganz [ctb],
David Whiting [ctb],
Crown Copyright 2018 [cph]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Diff between fingertipsR versions 1.0.0 dated 2020-01-07 and 1.0.1 dated 2020-01-28
DESCRIPTION | 6 MD5 | 58 +++---- NEWS.md | 8 - R/area_types.R | 7 R/deprivation_decile.R | 60 ++++---- R/fingertips_data.R | 36 ++++ R/retrieve_data.R | 76 +++------- inst/doc/lifeExpectancy.R | 54 +++---- inst/doc/lifeExpectancy.Rmd | 91 ++++++------ inst/doc/lifeExpectancy.html | 246 ++++++++++++++++----------------- inst/doc/selectIndicatorsRedRed.html | 10 - man/area_types.Rd | 132 ++++++++--------- man/category_types.Rd | 91 ++++++------ man/deprivation_decile.Rd | 121 ++++++++-------- man/fingertipsR.Rd | 2 man/fingertips_data.Rd | 188 ++++++++++++------------- man/fingertips_ensure_api_available.Rd | 2 man/fingertips_redred.Rd | 2 man/fingertips_stats.Rd | 2 man/indicator_areatypes.Rd | 2 man/indicator_metadata.Rd | 2 man/indicator_order.Rd | 110 +++++++------- man/indicators.Rd | 2 man/indicators_unique.Rd | 2 man/nearest_neighbours.Rd | 2 man/profiles.Rd | 2 man/select_indicators.Rd | 2 tests/testthat/test-deprivation.R | 165 ++-------------------- tests/testthat/test-extract.R | 140 ++++++++---------- vignettes/lifeExpectancy.Rmd | 91 ++++++------ 30 files changed, 792 insertions(+), 920 deletions(-)
Title: 'IUCN' Red List Client
Description: 'IUCN' Red List (<http://apiv3.iucnredlist.org/api/v3/docs>) client.
The 'IUCN' Red List is a global list of threatened and endangered species.
Functions cover all of the Red List 'API' routes. An 'API' key is required.
Author: Scott Chamberlain [aut, cre],
rOpenSci [fnd] (https://ropensci.org/),
Maëlle Salmon [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rredlist versions 0.5.0 dated 2018-07-19 and 0.6.0 dated 2020-01-28
rredlist-0.5.0/rredlist/tests/fixtures/vcr_cassettes |only rredlist-0.6.0/rredlist/DESCRIPTION | 24 + rredlist-0.6.0/rredlist/LICENSE | 2 rredlist-0.6.0/rredlist/MD5 | 148 +++++----- rredlist-0.6.0/rredlist/NEWS.md | 9 rredlist-0.6.0/rredlist/R/rl_citation.R | 2 rredlist-0.6.0/rredlist/R/rl_version.R | 2 rredlist-0.6.0/rredlist/R/rredlist-package.R | 7 rredlist-0.6.0/rredlist/R/zzz.R | 13 rredlist-0.6.0/rredlist/README.md | 64 ++-- rredlist-0.6.0/rredlist/man/rl_citation.Rd | 2 rredlist-0.6.0/rredlist/man/rl_growth_forms.Rd | 10 rredlist-0.6.0/rredlist/man/rl_habitats.Rd | 10 rredlist-0.6.0/rredlist/man/rl_history.Rd | 10 rredlist-0.6.0/rredlist/man/rl_measures.Rd | 10 rredlist-0.6.0/rredlist/man/rl_narrative.Rd | 10 rredlist-0.6.0/rredlist/man/rl_occ_country.Rd | 10 rredlist-0.6.0/rredlist/man/rl_search.Rd | 3 rredlist-0.6.0/rredlist/man/rl_sp.Rd | 3 rredlist-0.6.0/rredlist/man/rl_sp_citation.Rd | 10 rredlist-0.6.0/rredlist/man/rl_threats.Rd | 10 rredlist-0.6.0/rredlist/man/rl_version.Rd | 2 rredlist-0.6.0/rredlist/man/rredlist-package.Rd | 11 rredlist-0.6.0/rredlist/tests/fixtures/rl_citation.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_common_names-badkey.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_common_names-no-results.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_common_names-not-parsing.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_common_names.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_common_names_-badkey.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_common_names_.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_countries-not-parsing.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_countries.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_countries_.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_growth_forms-no-results.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_growth_forms-not-parsing.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_growth_forms.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_growth_forms_.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_habitats-not-found.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_habitats-not-parsing.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_habitats.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_habitats_-region-not-found.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_habitats_.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_history-by-id.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_history-not-parsing.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_history-region-together.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_history.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_history_.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_measures-no-results.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_measures-not-parsing.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_measures.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_measures_-region-not-found.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_measures_.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_narrative-no-results.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_narrative-not-parsing.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_narrative.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_narrative_.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_search-no-results.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_search-not-parsing.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_search.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_search_-region-not-found.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_search_.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_sp_category-no-results.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_sp_category-not-parsing.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_sp_category.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_sp_category_.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_synonyms-no-results.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_synonyms-not-parsing.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_synonyms.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_synonyms_.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_threats-no-results.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_threats-not-parsing.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_threats.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_threats_.yml |only rredlist-0.6.0/rredlist/tests/fixtures/rl_version.yml |only rredlist-0.6.0/rredlist/tests/testthat/helper-rredlist.R | 2 rredlist-0.6.0/rredlist/tests/testthat/test-rl_search.R | 3 76 files changed, 235 insertions(+), 142 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb],
Eamon O'Dea [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 2.4 dated 2019-10-21 and 2.5 dated 2020-01-28
DESCRIPTION | 20 +-- MD5 | 279 ++++++++++++++++++++++++------------------------- R/abc.R | 15 -- R/accumulators.R | 3 R/basic_probes.R | 9 - R/blowflies.R | 38 ++---- R/bsflu.R | 8 - R/bsmc2.R | 11 + R/dacca.R | 5 R/design.R | 10 - R/distributions.R | 9 - R/ebola.R | 15 -- R/forecast.R | 2 R/kalman.R | 11 - R/measles.R | 7 - R/mif2.R | 54 ++++----- R/nlf.R | 16 -- R/parus.R | 8 - R/pfilter.R | 52 +++++---- R/pmcmc.R | 14 +- R/pomp-package.R | 7 - R/pomp.R | 6 - R/pomp_examp.R |only R/probe.R | 10 - R/proposals.R | 6 - R/runif_design.R | 1 R/sir.R | 2 R/spect.R | 11 - data/LondonYorke.rda |binary data/bsflu.rda |binary data/ebolaWA2014.rda |binary data/ewcitmeas.rda |binary data/ewmeas.rda |binary inst/NEWS | 19 +++ inst/NEWS.Rd | 10 + man/abc.Rd | 91 ++++++++++----- man/accumulators.Rd | 148 ++++++++++++++++++++++++- man/as_data_frame.Rd | 1 man/basic_probes.Rd | 34 +++-- man/blowflies.Rd | 87 ++++++++------- man/bsflu.Rd | 28 +++- man/bsmc2.Rd | 70 ++++++++---- man/bsplines.Rd | 10 + man/concat.Rd | 1 man/cond_logLik.Rd | 15 +- man/continue.Rd | 1 man/covariate_table.Rd | 30 ++--- man/covmat.Rd | 13 -- man/csnippet.Rd | 24 ++-- man/dacca.Rd | 55 ++++++--- man/design.Rd | 19 +-- man/distributions.Rd | 32 ++--- man/dmeasure.Rd | 17 +- man/dmeasure_spec.Rd | 24 ++-- man/dprior.Rd | 17 +- man/dprocess.Rd | 17 +- man/dprocess_spec.Rd | 26 ++-- man/ebola.Rd | 63 ++++++----- man/eff_sample_size.Rd | 16 +- man/filter_mean.Rd | 15 +- man/filter_traj.Rd | 16 +- man/flow.Rd | 21 ++- man/forecast.Rd | 4 man/gompertz.Rd | 29 +++-- man/hitch.Rd | 18 ++- man/kalman.Rd | 61 ++++++---- man/loglik.Rd | 1 man/macros |only man/measles.Rd | 31 +++-- man/mif2.Rd | 109 +++++++++++++------ man/nlf.Rd | 98 +++++++++++------ man/ou2.Rd | 35 ++++-- man/parameter_trans.Rd | 27 ++-- man/partrans.Rd | 20 ++- man/parus.Rd | 30 +++-- man/pfilter.Rd | 81 +++++++++----- man/plot.Rd | 26 +++- man/pmcmc.Rd | 99 +++++++++++------ man/pomp-package.Rd | 52 +++++---- man/pomp.Rd | 38 +++++- man/pomp_examp.Rd |only man/pomp_fun.Rd | 39 +++++- man/pred_mean.Rd | 16 +- man/pred_var.Rd | 16 +- man/prior_spec.Rd | 25 ++-- man/probe.Rd | 67 +++++++---- man/probe_match.Rd | 85 ++++++++++---- man/proposals.Rd | 15 +- man/ricker.Rd | 18 ++- man/rinit.Rd | 17 +- man/rinit_spec.Rd | 27 ++-- man/rmeasure.Rd | 17 +- man/rmeasure_spec.Rd | 25 ++-- man/rprior.Rd | 17 +- man/rprocess.Rd | 17 +- man/rprocess_spec.Rd | 25 ++-- man/rw2.Rd | 21 ++- man/simulate.Rd | 60 +++++++--- man/sir.Rd | 58 +++++++--- man/skeleton.Rd | 17 +- man/skeleton_spec.Rd | 25 ++-- man/spect.Rd | 83 +++++++++----- man/spect_match.Rd | 91 +++++++++++---- man/spy.Rd | 1 man/summary.Rd | 1 man/time.Rd | 1 man/traces.Rd | 1 man/traj_match.Rd | 36 +++++- man/trajectory.Rd | 16 +- man/transformations.Rd | 25 ++-- man/undefined.Rd | 1 man/userdata.Rd | 27 ++-- man/verhulst.Rd | 21 ++- man/workhorses.Rd | 17 +- src/bspline.c | 16 +- src/distributions.c | 10 - src/dmeasure.c | 12 +- src/dprocess.c | 10 - src/euler.c | 12 +- src/init.c | 2 src/lookup_table.c | 2 src/ou2.c | 2 src/partrans.c | 2 src/pfilter.c | 145 ++++++++++++++++++------- src/pomp_decls.h | 2 src/pomp_fun.c | 2 src/pomp_internal.h | 3 src/probe.c | 12 +- src/probe_acf.c | 15 +- src/probe_marginal.c | 4 src/resample.c | 2 src/rinit.c | 8 - src/rmeasure.c | 12 +- src/rprior.c | 4 src/rprocess.c | 8 - src/simulate.c | 2 src/skeleton.c | 14 +- src/sobolseq.c | 4 src/ssa.c | 12 +- src/synth_lik.c | 6 - src/trajectory.c | 6 - src/userdata.c | 10 - 142 files changed, 2278 insertions(+), 1297 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell Lenth [aut, cre, cph],
Henrik Singmann [ctb],
Jonathon Love [ctb],
Paul Buerkner [ctb],
Maxime Herve [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.4.3.01 dated 2019-11-28 and 1.4.4 dated 2020-01-28
DESCRIPTION | 10 MD5 | 196 +++++----- NAMESPACE | 8 NEWS.md | 18 R/0nly-internal.R | 14 R/MCMC-support.R | 2 R/contrast.R | 1 R/countreg-support.R | 64 +++ R/emm-contr.R | 1 R/emm-list.R | 35 + R/emmGrid-methods.R | 6 R/emmeans-package.R | 4 R/emmeans.R | 15 R/emmip.R | 65 ++- R/glht-support.R | 1 R/helpers.R | 2 R/interfacing.R | 7 R/multinom-support.R | 2 R/nested.R | 29 + R/ordinal-support.R | 2 R/pwpp.R | 13 R/qdrg.R | 13 R/ref-grid.R | 8 R/rms-support.R | 2 R/test.R | 22 - inst/doc/FAQs.R | 6 inst/doc/FAQs.Rmd | 6 inst/doc/FAQs.html | 17 inst/doc/basics.R | 76 +-- inst/doc/basics.Rmd | 2 inst/doc/basics.html | 15 inst/doc/comparisons.R | 34 - inst/doc/comparisons.html | 19 inst/doc/confidence-intervals.R | 32 - inst/doc/confidence-intervals.html | 15 inst/doc/interactions.R | 44 +- inst/doc/interactions.html | 25 - inst/doc/messy-data.R | 48 +- inst/doc/messy-data.Rmd | 25 + inst/doc/messy-data.html | 22 - inst/doc/models.Rmd | 4 inst/doc/models.html | 9 inst/doc/predictions.html | 7 inst/doc/sophisticated.html | 11 inst/doc/transformations.R | 50 +- inst/doc/transformations.html | 7 inst/doc/utilities.R | 42 +- inst/doc/utilities.html | 7 inst/doc/vignette-topics.Rmd | 9 inst/doc/vignette-topics.html | 20 - inst/doc/xtending.R | 36 - inst/doc/xtending.Rmd | 2 inst/doc/xtending.html | 13 man/CLD.emmGrid.Rd | 178 ++++----- man/MOats.Rd | 90 ++-- man/add_grouping.Rd | 98 ++--- man/as.emmGrid.Rd | 136 +++---- man/auto.noise.Rd | 102 ++--- man/contrast.Rd | 368 +++++++++---------- man/eff_size.Rd | 240 ++++++------ man/emmGrid-class.Rd | 196 +++++----- man/emmGrid-methods.Rd | 56 +- man/emm_list-object.Rd | 56 +- man/emm_options.Rd | 246 ++++++------ man/emmc-functions.Rd | 335 ++++++++--------- man/emmeans-package.Rd | 198 +++++----- man/emmeans.Rd | 346 +++++++++--------- man/emmip.Rd | 261 +++++++------ man/emmobj.Rd | 174 ++++----- man/emtrends.Rd | 279 +++++++------- man/extending-emmeans.Rd | 394 ++++++++++---------- man/feedlot.Rd | 98 ++--- man/fiber.Rd | 78 ++-- man/glht-support.Rd | 154 ++++---- man/hpd.summary.Rd | 112 ++--- man/joint_tests.Rd | 170 ++++---- man/make.tran.Rd | 248 ++++++------ man/mcmc-support.Rd | 200 +++++----- man/models.Rd | 18 man/neuralgia.Rd | 82 ++-- man/nutrition.Rd | 98 ++--- man/oranges.Rd | 90 ++-- man/pigs.Rd | 64 +-- man/plot.Rd | 211 +++++------ man/pwpp.Rd | 174 ++++----- man/qdrg.Rd | 175 ++++----- man/rbind.emmGrid.Rd | 132 +++--- man/ref_grid.Rd | 678 +++++++++++++++++------------------ man/regrid.Rd | 256 ++++++------- man/summary.emmGrid.Rd | 707 ++++++++++++++++++------------------- man/update.emmGrid.Rd | 334 ++++++++--------- man/wrappers.Rd | 152 +++---- man/xtable.emmGrid.Rd | 129 +++--- vignettes/FAQs.Rmd | 6 vignettes/basics.Rmd | 2 vignettes/messy-data.Rmd | 25 + vignettes/models.Rmd | 4 vignettes/vignette-topics.Rmd | 9 vignettes/xtending.Rmd | 2 99 files changed, 4831 insertions(+), 4473 deletions(-)
Title: Meta-Analysis of Medians
Description: Implements several methods to meta-analyze studies that report the
sample median of the outcome. When the primary studies are one-group
studies, the methods of McGrath et al. (2019) <doi:10.1002/sim.8013> can
be applied to estimate the pooled median. In the two-group context, the
methods of McGrath et al. (2020) <doi:10.1002/bimj.201900036> can be
applied to estimate the pooled raw difference of medians across groups.
Author: Sean McGrath [aut, cre] (<https://orcid.org/0000-0002-7281-3516>),
XiaoFei Zhao [aut],
Russell Steele [aut],
Andrea Benedetti [aut] (<https://orcid.org/0000-0002-8314-9497>)
Maintainer: Sean McGrath <sean.mcgrath@mail.mcgill.ca>
Diff between metamedian versions 0.1.4 dated 2019-05-19 and 0.1.5 dated 2020-01-28
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 8 +++++++- R/pool.med.R | 27 +++++++++++++++------------ R/qe.R | 4 ++-- R/qe.study.level.R | 4 ++-- README.md | 3 ++- man/pool.med.Rd | 14 ++++++++------ man/qe.Rd | 4 ++-- man/qe.study.level.Rd | 4 ++-- 10 files changed, 54 insertions(+), 42 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-12 2015.6.26.2
2019-03-02 2015.6.26.1
2015-06-27 2015.6.26
2012-04-10 2012.04-0
2011-02-11 0.1-7.1
2009-10-22 0.1-7
2009-02-12 0.1-6
2007-09-30 0.1-4
2007-03-08 0.1-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-14 1.0.0
2019-04-16 0.92.6
2019-03-15 0.92.5
2019-02-08 0.92.4
2018-02-07 0.92.3
2017-10-13 0.92.0
2017-10-06 0.91.0
2017-08-04 0.90.0
2017-06-09 0.82.6
2017-05-04 0.82.5
2017-04-03 0.82.3
2017-02-17 0.82.2
2016-10-13 0.80.14
2016-10-11 0.80.13