Title: Installing, Managing, and Switching Between Distinct Sets of
Installed Packages
Description: Provides an abstraction for managing, installing,
and switching between sets of installed R packages. This allows users to
maintain multiple package libraries simultaneously, e.g. to maintain
strict, package-version-specific reproducibility of many analyses, or
work within a devel/release paradigm. Introduces a generalized package
installation process which supports multiple repository and
non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between switchr versions 0.9.3 dated 2015-06-03 and 0.9.4 dated 2015-06-05
DESCRIPTION | 6 ++--- MD5 | 21 ++++++++++--------- NEWS |only R/Utilities.R | 2 - R/accessors.R | 4 --- R/findCtx.R | 3 +- R/lazyRepo.R | 31 ++++++++++++++++++++++++++++ R/loadManifest.R | 2 - R/makePkgSourceDir-methods.R | 5 ++-- R/methods.R | 47 ++++++++++++++++++++++++++++++++++--------- inst/doc/switchrvign.pdf |binary man/lazyRepo.Rd | 7 ++++++ 12 files changed, 97 insertions(+), 31 deletions(-)
Title: Query 'R' Versions, Including 'r-release' and 'r-oldrel'
Description: Query the main 'R' 'SVN' repository to find the
versions 'r-release' and 'r-oldrel' refer to, and also all
previous 'R' versions and their release dates.
Author: Gabor Csardi [aut, cre],
Jeroen Ooms [ctb]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rversions versions 1.0.0 dated 2015-04-22 and 1.0.1 dated 2015-06-05
DESCRIPTION | 23 +++++++++++--------- MD5 | 14 +++++++----- NAMESPACE | 16 +++++++------- R/rversions.R | 61 ++++++++++++++++++++++++------------------------------ inst |only man/r_oldrel.Rd | 2 - man/r_release.Rd | 2 - man/r_versions.Rd | 2 - 8 files changed, 61 insertions(+), 59 deletions(-)
Title: Two Stage Least Squares with Model Implied Instrumental Search
Description: Functions for estimating structural equation models
using a model-implied instrumental variable (MIIV) search
and two stage least squares (2SLS) estimator (MIIV-2SLS).
Author: Zachary Fisher and Ken Bollen.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.1 dated 2015-04-10 and 0.2 dated 2015-06-05
DESCRIPTION | 10 - MD5 | 24 +-- NAMESPACE | 3 R/MIIVsem-data.R | 8 - R/MIIVsem.R | 2 R/miive.R | 356 +++++++++++++++++++++++++++++++++++++++++------------ R/miivs.R | 214 +++++++++++++++++++------------ R/print.miive.R | 72 +++++++++- R/print.miivs.R | 1 man/MIIVsem.Rd | 2 man/bollen1989a.Rd | 8 - man/miive.Rd | 12 + man/miivs.Rd | 5 13 files changed, 516 insertions(+), 201 deletions(-)
Title: Interactive Grammar of Graphics
Description: An implementation of an interactive grammar of graphics, taking the
best parts of 'ggplot2', combining them with the reactive framework from
'shiny' and web graphics from 'vega'.
Author: Winston Chang [aut, cre],
Hadley Wickham [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/lib/jquery/AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/lib/jquery-ui/AUTHORS.txt),
Mike Bostock [ctb, cph] (D3 library),
D3 contributors [ctb] (D3 library; authors listed at
https://github.com/mbostock/d3/graphs/contributors),
Trifacta Inc. [cph] (Vega library),
Vega contributors [ctb] (Vega library; authors listed at
https://github.com/trifacta/vega/graphs/contributors),
Sebasti<c3><a1>n D<c3><a9>cima [ctb, cph]
(javascript-detect-element-resize library)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between ggvis versions 0.4.1 dated 2015-03-12 and 0.4.2 dated 2015-06-05
ggvis-0.4.1/ggvis/inst/www/lib/jquery-ui/css |only ggvis-0.4.1/ggvis/inst/www/lib/jquery-ui/js |only ggvis-0.4.2/ggvis/DESCRIPTION | 22 ggvis-0.4.2/ggvis/LICENSE | 29 ggvis-0.4.2/ggvis/MD5 | 335 ggvis-0.4.2/ggvis/NAMESPACE | 2 ggvis-0.4.2/ggvis/R/compute_stack.R | 18 ggvis-0.4.2/ggvis/R/ggvis_html.R | 12 ggvis-0.4.2/ggvis/R/options.R | 27 ggvis-0.4.2/ggvis/R/shiny_layout.R | 4 ggvis-0.4.2/ggvis/R/vega.R | 2 ggvis-0.4.2/ggvis/build/vignette.rds |binary ggvis-0.4.2/ggvis/demo/apps/basic/server.r | 4 ggvis-0.4.2/ggvis/demo/apps/basic/ui.r | 4 ggvis-0.4.2/ggvis/inst/doc/axes-legends.R | 20 ggvis-0.4.2/ggvis/inst/doc/axes-legends.html | 3025 +-- ggvis-0.4.2/ggvis/inst/doc/cookbook.R | 32 ggvis-0.4.2/ggvis/inst/doc/cookbook.html | 5526 +++--- ggvis-0.4.2/ggvis/inst/doc/data-hierarchy.R | 6 ggvis-0.4.2/ggvis/inst/doc/ggplot2.R | 2 ggvis-0.4.2/ggvis/inst/doc/ggvis-basics.R | 4 ggvis-0.4.2/ggvis/inst/doc/ggvis-basics.html | 8902 ++++------ ggvis-0.4.2/ggvis/inst/doc/interactivity.R | 10 ggvis-0.4.2/ggvis/inst/doc/interactivity.html | 1493 - ggvis-0.4.2/ggvis/inst/doc/layers.R | 4 ggvis-0.4.2/ggvis/inst/doc/layers.html | 3402 +-- ggvis-0.4.2/ggvis/inst/doc/overview.R | 6 ggvis-0.4.2/ggvis/inst/doc/overview.html | 554 ggvis-0.4.2/ggvis/inst/doc/properties-scales.R | 12 ggvis-0.4.2/ggvis/inst/doc/properties-scales.html | 2234 +- ggvis-0.4.2/ggvis/inst/www/ggvis/css/ggvis.css | 3 ggvis-0.4.2/ggvis/inst/www/ggvis/js/ggvis.js | 127 ggvis-0.4.2/ggvis/inst/www/lib/detect-resize |only ggvis-0.4.2/ggvis/inst/www/lib/jquery-ui/AUTHORS.txt | 46 ggvis-0.4.2/ggvis/inst/www/lib/jquery-ui/images |only ggvis-0.4.2/ggvis/inst/www/lib/jquery-ui/jquery-ui.min.css |only ggvis-0.4.2/ggvis/inst/www/lib/jquery-ui/jquery-ui.min.js |only ggvis-0.4.2/ggvis/man/add_axis.Rd | 2 ggvis-0.4.2/ggvis/man/add_data.Rd | 2 ggvis-0.4.2/ggvis/man/add_guide_axis.Rd | 2 ggvis-0.4.2/ggvis/man/add_guide_legend.Rd | 2 ggvis-0.4.2/ggvis/man/add_legend.Rd | 2 ggvis-0.4.2/ggvis/man/add_props.Rd | 2 ggvis-0.4.2/ggvis/man/add_relative_scales.Rd | 2 ggvis-0.4.2/ggvis/man/add_scale.Rd | 2 ggvis-0.4.2/ggvis/man/add_tooltip.Rd | 2 ggvis-0.4.2/ggvis/man/as.vega.Rd | 2 ggvis-0.4.2/ggvis/man/auto_group.Rd | 2 ggvis-0.4.2/ggvis/man/axis_props.Rd | 2 ggvis-0.4.2/ggvis/man/band.Rd | 2 ggvis-0.4.2/ggvis/man/bin_vector.Rd | 2 ggvis-0.4.2/ggvis/man/cocaine.Rd | 2 ggvis-0.4.2/ggvis/man/compute_align.Rd | 2 ggvis-0.4.2/ggvis/man/compute_bin.Rd | 2 ggvis-0.4.2/ggvis/man/compute_boxplot.Rd | 2 ggvis-0.4.2/ggvis/man/compute_count.Rd | 2 ggvis-0.4.2/ggvis/man/compute_density.Rd | 2 ggvis-0.4.2/ggvis/man/compute_model_prediction.Rd | 2 ggvis-0.4.2/ggvis/man/compute_stack.Rd | 2 ggvis-0.4.2/ggvis/man/compute_tabulate.Rd | 2 ggvis-0.4.2/ggvis/man/create_broker.Rd | 2 ggvis-0.4.2/ggvis/man/create_input.Rd | 2 ggvis-0.4.2/ggvis/man/default_options.Rd | 2 ggvis-0.4.2/ggvis/man/dplyr-ggvis.Rd | 2 ggvis-0.4.2/ggvis/man/explain.Rd | 2 ggvis-0.4.2/ggvis/man/explain.ggvis.Rd | 2 ggvis-0.4.2/ggvis/man/export_png.Rd | 2 ggvis-0.4.2/ggvis/man/fullseq.Rd | 2 ggvis-0.4.2/ggvis/man/get_data.Rd | 2 ggvis-0.4.2/ggvis/man/ggvis.Rd | 2 ggvis-0.4.2/ggvis/man/ggvisControlOutput.Rd | 2 ggvis-0.4.2/ggvis/man/ggvisOutputElements.Rd | 2 ggvis-0.4.2/ggvis/man/ggvis_message.Rd | 2 ggvis-0.4.2/ggvis/man/ggvis_scale.Rd | 2 ggvis-0.4.2/ggvis/man/group_by.Rd | 2 ggvis-0.4.2/ggvis/man/handle_brush.Rd | 2 ggvis-0.4.2/ggvis/man/handle_click.Rd | 2 ggvis-0.4.2/ggvis/man/handle_resize.Rd | 2 ggvis-0.4.2/ggvis/man/input_checkbox.Rd | 2 ggvis-0.4.2/ggvis/man/input_select.Rd | 2 ggvis-0.4.2/ggvis/man/input_slider.Rd | 2 ggvis-0.4.2/ggvis/man/input_text.Rd | 2 ggvis-0.4.2/ggvis/man/is.axis_props.Rd | 2 ggvis-0.4.2/ggvis/man/is.broker.Rd | 2 ggvis-0.4.2/ggvis/man/is.dynamic.Rd | 2 ggvis-0.4.2/ggvis/man/is.ggvis.Rd | 2 ggvis-0.4.2/ggvis/man/is.legend_props.Rd | 2 ggvis-0.4.2/ggvis/man/is.scaled_value.Rd | 2 ggvis-0.4.2/ggvis/man/knit_print.ggvis.Rd | 2 ggvis-0.4.2/ggvis/man/layer_bars.Rd | 2 ggvis-0.4.2/ggvis/man/layer_boxplots.Rd | 2 ggvis-0.4.2/ggvis/man/layer_densities.Rd | 2 ggvis-0.4.2/ggvis/man/layer_f.Rd | 2 ggvis-0.4.2/ggvis/man/layer_guess.Rd | 2 ggvis-0.4.2/ggvis/man/layer_histograms.Rd | 2 ggvis-0.4.2/ggvis/man/layer_lines.Rd | 2 ggvis-0.4.2/ggvis/man/layer_model_predictions.Rd | 2 ggvis-0.4.2/ggvis/man/left_right.Rd | 2 ggvis-0.4.2/ggvis/man/legend_props.Rd | 2 ggvis-0.4.2/ggvis/man/linked_brush.Rd | 2 ggvis-0.4.2/ggvis/man/mark.Rd | 2 ggvis-0.4.2/ggvis/man/marks.Rd | 2 ggvis-0.4.2/ggvis/man/new_prop.Rd | 2 ggvis-0.4.2/ggvis/man/padding.Rd | 2 ggvis-0.4.2/ggvis/man/pipe.Rd | 2 ggvis-0.4.2/ggvis/man/print.ggvis.Rd | 2 ggvis-0.4.2/ggvis/man/prop.Rd | 2 ggvis-0.4.2/ggvis/man/prop_domain.Rd | 2 ggvis-0.4.2/ggvis/man/propname_to_scale.Rd | 2 ggvis-0.4.2/ggvis/man/props.Rd | 2 ggvis-0.4.2/ggvis/man/resolution.Rd | 2 ggvis-0.4.2/ggvis/man/save_spec.Rd | 2 ggvis-0.4.2/ggvis/man/scale_datetime.Rd | 2 ggvis-0.4.2/ggvis/man/scale_numeric.Rd | 2 ggvis-0.4.2/ggvis/man/scale_ordinal.Rd | 2 ggvis-0.4.2/ggvis/man/scaled_value.Rd | 2 ggvis-0.4.2/ggvis/man/scales.Rd | 2 ggvis-0.4.2/ggvis/man/scaletype_to_vega_scaletype.Rd | 2 ggvis-0.4.2/ggvis/man/set_options.Rd | 31 ggvis-0.4.2/ggvis/man/set_scale_label.Rd | 2 ggvis-0.4.2/ggvis/man/shiny-ggvis.Rd | 2 ggvis-0.4.2/ggvis/man/show_spec.Rd | 2 ggvis-0.4.2/ggvis/man/show_tooltip.Rd | 2 ggvis-0.4.2/ggvis/man/sidebarBottomPage.Rd | 2 ggvis-0.4.2/ggvis/man/singular.Rd | 2 ggvis-0.4.2/ggvis/man/subvis.Rd | 2 ggvis-0.4.2/ggvis/man/vector_type.Rd | 2 ggvis-0.4.2/ggvis/man/vega_data_parser.Rd | 2 ggvis-0.4.2/ggvis/man/waggle.Rd | 2 ggvis-0.4.2/ggvis/man/zero_range.Rd | 2 ggvis-0.4.2/ggvis/tests/specs/bar/categorical-x.json | 249 ggvis-0.4.2/ggvis/tests/specs/bar/continuous-x.json | 251 ggvis-0.4.2/ggvis/tests/specs/boxplot/boxplot-categorical.json | 609 ggvis-0.4.2/ggvis/tests/specs/boxplot/boxplot-continuous.json | 567 ggvis-0.4.2/ggvis/tests/specs/boxplot/boxplot-no-outliers.json | 609 ggvis-0.4.2/ggvis/tests/specs/data/dots.json | 319 ggvis-0.4.2/ggvis/tests/specs/layer/freqpoly-grouped.json | 322 ggvis-0.4.2/ggvis/tests/specs/layer/histogram.json | 251 ggvis-0.4.2/ggvis/tests/specs/layer/smooth-grouped.json | 277 ggvis-0.4.2/ggvis/tests/specs/layer/smooth.json | 237 ggvis-0.4.2/ggvis/tests/specs/line/basic.json | 225 ggvis-0.4.2/ggvis/tests/specs/line/layer-line-nominal-x.json | 313 ggvis-0.4.2/ggvis/tests/specs/line/layer-line.json | 313 ggvis-0.4.2/ggvis/tests/specs/line/sort.json | 225 ggvis-0.4.2/ggvis/tests/specs/scales/bars.json | 249 ggvis-0.4.2/ggvis/tests/specs/scales/combined_legend.json | 331 ggvis-0.4.2/ggvis/tests/specs/scales/custom.json | 286 ggvis-0.4.2/ggvis/tests/specs/scales/datetime.json | 229 ggvis-0.4.2/ggvis/tests/specs/scales/datetime_hist.json | 249 ggvis-0.4.2/ggvis/tests/specs/scales/domain_numeric.json | 286 ggvis-0.4.2/ggvis/tests/specs/scales/dual.json | 325 ggvis-0.4.2/ggvis/tests/specs/scales/hide_guides.json | 300 ggvis-0.4.2/ggvis/tests/specs/scales/log.json | 233 ggvis-0.4.2/ggvis/tests/specs/scatter/basic.json | 229 ggvis-0.4.2/ggvis/tests/specs/scatter/fill-continuous.json | 288 ggvis-0.4.2/ggvis/tests/specs/scatter/fill-discrete.json | 283 ggvis-0.4.2/ggvis/tests/specs/scatter/transform.json | 231 ggvis-0.4.2/ggvis/tools |only 158 files changed, 16697 insertions(+), 17671 deletions(-)
Title: Fast Algorithms to Bootstrap Receiver Operating Characteristics
Curves
Description: Implements a very fast C++ algorithm to quickly bootstrap
receiver operating characteristics (ROC) curves and derived performance metrics, including the area under the
curve (AUC) as well as the true and false positive rate.
You can also plot the results and calculate confidence intervals.
Currently the calculation of 100000 bootstrap replicates for 500 observations
takes about one second.
Author: Erik Peter [aut, cre]
Maintainer: Erik Peter <jerikpeter@googlemail.com>
Diff between fbroc versions 0.1.0 dated 2015-05-05 and 0.2.0 dated 2015-06-05
fbroc-0.1.0/fbroc/man/calculate.thresholds.Rd |only fbroc-0.1.0/fbroc/src/rocboot.cpp |only fbroc-0.2.0/fbroc/DESCRIPTION | 19 +-- fbroc-0.2.0/fbroc/MD5 | 52 +++++--- fbroc-0.2.0/fbroc/NAMESPACE | 1 fbroc-0.2.0/fbroc/R/RcppExports.R | 36 +++-- fbroc-0.2.0/fbroc/R/fbroc.R | 26 ++-- fbroc-0.2.0/fbroc/R/fbroc.data.doc.R |only fbroc-0.2.0/fbroc/R/fbroc.methods.R | 69 +++++++---- fbroc-0.2.0/fbroc/R/fbroc.perf.R | 61 ++++++++- fbroc-0.2.0/fbroc/R/fbroc.roc.R | 162 +++++++++++++------------- fbroc-0.2.0/fbroc/README.md | 5 fbroc-0.2.0/fbroc/data |only fbroc-0.2.0/fbroc/man/boot.roc.Rd | 42 ++++-- fbroc-0.2.0/fbroc/man/boot.tpr.at.fpr.Rd | 13 -- fbroc-0.2.0/fbroc/man/conf.roc.Rd | 4 fbroc-0.2.0/fbroc/man/fbroc.Rd | 25 ++-- fbroc-0.2.0/fbroc/man/perf.roc.Rd | 10 + fbroc-0.2.0/fbroc/man/plot.fbroc.perf.Rd | 4 fbroc-0.2.0/fbroc/man/plot.fbroc.roc.Rd | 2 fbroc-0.2.0/fbroc/man/roc.examples.Rd |only fbroc-0.2.0/fbroc/src/RcppExports.cpp | 106 ++++++++++++----- fbroc-0.2.0/fbroc/src/bootstrapper.cpp |only fbroc-0.2.0/fbroc/src/bootstrapper.h |only fbroc-0.2.0/fbroc/src/disc_roc.cpp |only fbroc-0.2.0/fbroc/src/interface.common.cpp |only fbroc-0.2.0/fbroc/src/interface.common.h |only fbroc-0.2.0/fbroc/src/interface.paired.cpp |only fbroc-0.2.0/fbroc/src/interface.single.cpp |only fbroc-0.2.0/fbroc/src/paired.roc.cpp |only fbroc-0.2.0/fbroc/src/paired.roc.h |only fbroc-0.2.0/fbroc/src/performance.cpp |only fbroc-0.2.0/fbroc/src/performance.h |only fbroc-0.2.0/fbroc/src/roc.cpp |only fbroc-0.2.0/fbroc/src/roc.h |only fbroc-0.2.0/fbroc/src/sampler.cpp |only fbroc-0.2.0/fbroc/src/sampler.h |only 37 files changed, 412 insertions(+), 225 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.6-0 dated 2015-04-03 and 1.7-1 dated 2015-06-05
TAM-1.6-0/TAM/data/sim.facets.rda |only TAM-1.6-0/TAM/data/sim.mfr.rda |only TAM-1.6-0/TAM/data/sim.rasch.missing.rda |only TAM-1.6-0/TAM/data/sim.rasch.pweights.rda |only TAM-1.6-0/TAM/data/sim.rasch.rda |only TAM-1.6-0/TAM/inst/sim.facets.R |only TAM-1.6-0/TAM/inst/sim.mfr.R |only TAM-1.6-0/TAM/inst/sim.rasch.R |only TAM-1.6-0/TAM/inst/sim.rasch.missing.R |only TAM-1.6-0/TAM/inst/sim.rasch.pweights.R |only TAM-1.6-0/TAM/man/sim.mfr.Rd |only TAM-1.6-0/TAM/man/sim.rasch.Rd |only TAM-1.7-1/TAM/DESCRIPTION | 14 TAM-1.7-1/TAM/MD5 | 127 ++++---- TAM-1.7-1/TAM/NAMESPACE | 20 + TAM-1.7-1/TAM/R/IRT.residuals.R |only TAM-1.7-1/TAM/R/TAM_utils.R |only TAM-1.7-1/TAM/R/calc_prob.v5.R | 2 TAM-1.7-1/TAM/R/mfr.dataprep.R | 40 +- TAM-1.7-1/TAM/R/msq.itemfit.R | 18 - TAM-1.7-1/TAM/R/msq.itemfitWLE.R |only TAM-1.7-1/TAM/R/plot.tam.R | 5 TAM-1.7-1/TAM/R/plotDevianceTAM.R | 18 - TAM-1.7-1/TAM/R/summary.msq.itemfit.R | 24 + TAM-1.7-1/TAM/R/summary.msq.itemfitWLE.R |only TAM-1.7-1/TAM/R/summary.tam.Q3.R |only TAM-1.7-1/TAM/R/summary.tam.R | 17 - TAM-1.7-1/TAM/R/summary.tam.modelfit.R |only TAM-1.7-1/TAM/R/tam.Q3.R |only TAM-1.7-1/TAM/R/tam.calc.counts.R | 1 TAM-1.7-1/TAM/R/tam.mml.2pl.R | 3 TAM-1.7-1/TAM/R/tam.mml.3pl.R | 44 +- TAM-1.7-1/TAM/R/tam.mml.3pl.algorithm.R | 10 TAM-1.7-1/TAM/R/tam.mml.3pl.est.slopes.R | 13 TAM-1.7-1/TAM/R/tam.mml.R | 11 TAM-1.7-1/TAM/R/tam.mml.mfr.R | 15 TAM-1.7-1/TAM/R/tam.modelfit.R | 56 ++- TAM-1.7-1/TAM/R/tam.wle.R | 40 +- TAM-1.7-1/TAM/R/tamaan.3pl.lca.R | 6 TAM-1.7-1/TAM/data/data.sim.facets.rda |only TAM-1.7-1/TAM/data/data.sim.mfr.rda |only TAM-1.7-1/TAM/data/data.sim.rasch.missing.rda |only TAM-1.7-1/TAM/data/data.sim.rasch.pweights.rda |only TAM-1.7-1/TAM/data/data.sim.rasch.rda |only TAM-1.7-1/TAM/inst/NEWS | 320 +++++++++++---------- TAM-1.7-1/TAM/man/IRT.WrightMap.Rd | 9 TAM-1.7-1/TAM/man/IRT.data.tam.Rd | 10 TAM-1.7-1/TAM/man/IRT.drawPV.Rd | 4 TAM-1.7-1/TAM/man/IRT.expectedCounts.tam.Rd | 12 TAM-1.7-1/TAM/man/IRT.factor.scores.tam.Rd | 12 TAM-1.7-1/TAM/man/IRT.irfprob.tam.Rd | 12 TAM-1.7-1/TAM/man/IRT.likelihood.tam.Rd | 12 TAM-1.7-1/TAM/man/IRT.residuals.Rd |only TAM-1.7-1/TAM/man/IRT.threshold.Rd | 9 TAM-1.7-1/TAM/man/IRTLikelihood.cfa.Rd | 2 TAM-1.7-1/TAM/man/TAM-package.Rd | 8 TAM-1.7-1/TAM/man/anova.tam.Rd | 6 TAM-1.7-1/TAM/man/cfa.extract.itempars.Rd | 6 TAM-1.7-1/TAM/man/data.cqc.Rd | 13 TAM-1.7-1/TAM/man/data.sim.mfr.Rd |only TAM-1.7-1/TAM/man/data.sim.rasch.Rd |only TAM-1.7-1/TAM/man/designMatrices.Rd | 2 TAM-1.7-1/TAM/man/lavaanify.IRT.Rd | 10 TAM-1.7-1/TAM/man/msq.itemfit.Rd | 148 ++++++++- TAM-1.7-1/TAM/man/plot.tam.Rd | 18 - TAM-1.7-1/TAM/man/plotDevianceTAM.Rd | 12 TAM-1.7-1/TAM/man/predict.Rd | 10 TAM-1.7-1/TAM/man/tam.fit.Rd | 14 TAM-1.7-1/TAM/man/tam.jml.Rd | 4 TAM-1.7-1/TAM/man/tam.mml.3pl.Rd | 14 TAM-1.7-1/TAM/man/tam.mml.Rd | 44 +- TAM-1.7-1/TAM/man/tam.modelfit.Rd | 66 +++- TAM-1.7-1/TAM/man/tam.pv.Rd | 4 TAM-1.7-1/TAM/man/tam.se.Rd | 6 TAM-1.7-1/TAM/man/tam.threshold.Rd | 4 TAM-1.7-1/TAM/man/tam.wle.Rd | 21 - TAM-1.7-1/TAM/man/tamaanify.Rd | 21 - TAM-1.7-1/TAM/src/tam_mml_3pl_helper_functions.cpp | 117 +++++++ 78 files changed, 963 insertions(+), 471 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.5.100.1.0 dated 2015-05-01 and 0.5.200.1.0 dated 2015-06-05
ChangeLog | 26 ++ DESCRIPTION | 10 MD5 | 48 ++-- README.md | 2 inst/NEWS.Rd | 19 + inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/examples/fastLm.r | 46 ++++ inst/include/RcppArmadilloAs.h | 38 +-- inst/include/armadillo_bits/Col_bones.hpp | 7 inst/include/armadillo_bits/Col_meat.hpp | 114 +++++----- inst/include/armadillo_bits/Mat_bones.hpp | 16 + inst/include/armadillo_bits/Mat_meat.hpp | 270 ++++++++++++++++++------- inst/include/armadillo_bits/Row_bones.hpp | 7 inst/include/armadillo_bits/Row_meat.hpp | 114 +++++----- inst/include/armadillo_bits/arma_rng.hpp | 45 ++-- inst/include/armadillo_bits/arma_version.hpp | 4 inst/include/armadillo_bits/cond_rel_bones.hpp | 2 inst/include/armadillo_bits/cond_rel_meat.hpp | 22 ++ inst/include/armadillo_bits/diskio_meat.hpp | 60 +++-- inst/include/armadillo_bits/fn_misc.hpp | 30 ++ inst/include/armadillo_bits/fn_rank.hpp | 44 +--- inst/include/armadillo_bits/op_misc_bones.hpp | 14 + inst/include/armadillo_bits/op_misc_meat.hpp | 57 +++++ inst/include/armadillo_bits/span.hpp | 3 25 files changed, 690 insertions(+), 308 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
G.C. Shen;
V. Shcherbakov;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@uwa.edu.au>
Diff between spatstat versions 1.42-0 dated 2015-06-01 and 1.42-1 dated 2015-06-05
DESCRIPTION | 10 ++++---- MD5 | 44 ++++++++++++++++++------------------- NAMESPACE | 4 +++ NEWS | 45 ++++++++++++++++++++++++++++++++++++++ R/boundingbox.R | 7 +++++ R/hyperframe.R | 31 ++++++++++++++++++-------- R/hypersub.R | 2 - R/measures.R | 4 ++- R/mppm.R | 25 +++++++++++---------- R/randomNS.R | 17 +++++++++++--- R/solist.R | 53 ++++++++++++++++++++++++--------------------- R/util.R | 18 ++++++++++++--- R/window.R | 5 ++++ inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.pdf |binary man/boundingbox.Rd | 5 ++++ man/rNeymanScott.Rd | 10 +++++++- man/rpoispp.Rd | 3 +- man/spatstat-internal.Rd | 4 +++ vignettes/packagesizes.txt | 1 23 files changed, 207 insertions(+), 81 deletions(-)
Title: Multinomial Logit Model
Description: Time and memory efficient estimation of multinomial logit models using maximum likelihood method. Numerical optimization performed by Newton-Raphson method using an optimized, parallel C++ library to achieve fast computation of Hessian matrices. Motivated by large scale multiclass classification problems in econometrics and machine learning.
Author: Asad Hasan, Wang Zhiyu, Alireza S. Mahani
Maintainer: Asad Hasan <asad.hasan@sentrana.com>
Diff between mnlogit versions 1.2.1 dated 2015-05-13 and 1.2.2 dated 2015-06-05
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/mnlogit.R | 4 +++- man/hyptests.Rd | 2 +- man/mnlogit.Rd | 2 +- 6 files changed, 18 insertions(+), 12 deletions(-)
Title: Supplementary Item Response Theory Models
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, faceted and hierarchical rater models,
ordinal IRT model (ISOP), discrete grade of membership model,
latent regression models, DETECT statistic, local structural
equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between sirt versions 1.6-0 dated 2015-05-20 and 1.7-0 dated 2015-06-05
DESCRIPTION | 8 - MD5 | 57 ++++---- NAMESPACE | 5 R/btm.R |only R/btm_fit.R |only R/categorize.R | 6 R/lsem.estimate.R | 12 - R/lsem.parameter.summary.R | 2 R/lsem.permutationTest.R | 5 R/osink.R |only R/plot.lsem.permutationTest.R | 21 ++- R/summary.btm.R |only R/summary.lsem.R | 15 +- R/summary.lsem.permutationTest.R | 15 +- data/data.pw01.rda |only inst/NEWS | 18 ++ man/brm.sim.Rd | 2 man/btm.Rd |only man/categorize.Rd | 2 man/data.pw01.Rd |only man/lavaan2mirt.Rd | 16 +- man/lsem.estimate.Rd | 6 man/lsem.permutationTest.Rd | 16 +- man/mirt.wrapper.Rd | 18 +- man/modelfit.sirt.Rd | 20 +- man/noharm.sirt.Rd | 2 man/pcm.conversion.Rd | 2 man/personfit.stat.Rd | 6 man/rasch.mirtlc.Rd | 3 man/rasch.mml.Rd | 2 man/sirt-package.Rd | 266 +++++++++++++++++++-------------------- man/tam2mirt.Rd | 2 man/testlet.marginalized.Rd | 4 33 files changed, 299 insertions(+), 232 deletions(-)
Title: Patient-Centered Network Meta-Analysis
Description: Provides functions to perform arm-based network meta-analysis for datasets with binary, continuous, and count outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin <linl@umn.edu>
Diff between pcnetmeta versions 2.2 dated 2015-05-13 and 2.2.1 dated 2015-06-05
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- man/absolute.plot.Rd | 3 ++- man/contrast.plot.Rd | 3 ++- man/nma.ab.Rd | 3 ++- man/nma.ab.cont.Rd | 3 ++- man/nma.ab.followup.Rd | 3 ++- man/nma.ab.py.Rd | 3 ++- man/rank.prob.Rd | 5 +++-- 9 files changed, 27 insertions(+), 20 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre],
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 1.0-22 dated 2015-03-14 and 1.0-23 dated 2015-06-05
DESCRIPTION | 12 MD5 | 110 NAMESPACE | 1 R/krige0.R | 207 R/krigeTg.R | 2 R/stVariogramModels.R | 84 R/variogramST.R | 6 build/vignette.rds |binary configure | 7146 ++++++++++++++++++++++++---------- configure.in | 2 data/coalash.rda |binary data/fulmar.rda |binary data/jura.rda |binary data/meuse.all.rda |binary data/meuse.alt.rda |binary data/ncp.grid.rda |binary data/oxford.rda |binary data/pcb.rda |binary data/sic2004.rda |binary data/sic97.rda |binary data/tull.rda |binary data/vv.rda |binary data/walker.rda |binary data/wind.rda |binary demo/00Index | 1 demo/localKrigeST.R | 27 demo/stkrige.R | 75 demo/zonal.R |only inst/doc/gstat.pdf |binary inst/doc/prs.Rnw | 380 - inst/doc/prs.pdf |binary inst/doc/spatio-temporal-kriging.Rnw |only inst/doc/spatio-temporal-kriging.pdf |only inst/doc/st.pdf |binary man/get.contr.Rd | 4 man/gstat.Rd | 34 man/krige.Rd | 14 man/krige.cv.Rd | 4 man/krigeST.Rd | 7 man/krigeTg.Rd | 6 man/map.to.lev.Rd | 4 man/predict.gstat.Rd | 12 man/vgmST.Rd | 9 man/vv.Rd | 3 src/meschach/dmacheps.c | 2 src/meschach/fmacheps.c | 2 src/meschach/maxint.c | 2 src/nsearch.c | 15 tests/merge.R | 4 tests/merge.Rout.save | 12 tests/unproj.R | 1 tests/unproj.Rout.save | 70 tests/windst.Rout.save | 19 vignettes/figures |only vignettes/prs.Rnw | 380 - vignettes/spatio-temporal-kriging.Rnw |only vignettes/spatio-temporal-kriging.bib |only 57 files changed, 6014 insertions(+), 2643 deletions(-)
Title: Basic Statistical Functions for Package 'ff'
Description: Extends the out of memory vectors of 'ff' with
statistical functions and other utilities to ease their usage.
Author: Edwin de Jonge, Jan Wijffels, Jan van der Laan
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between ffbase versions 0.12.0 dated 2015-05-25 and 0.12.1 dated 2015-06-05
DESCRIPTION | 8 ++++---- MD5 | 41 +++++++++++++++++++++-------------------- NAMESPACE | 12 ++++++++++++ NEWS | 3 +++ R/Summary_ff.R | 6 ++++++ R/compact.R | 2 +- R/cumsum.R | 9 +++++---- R/droplevels.R | 4 ++-- R/ffappend.R | 6 +++--- R/ffrep.R | 2 +- R/merge.R | 4 ++-- R/quantile_ff.R | 1 + R/rbind_ffdf.R | 4 ++-- R/save_ffdf.R | 12 ++++++------ R/subset.R | 2 +- R/table_ff.R | 2 ++ R/tabulate_ff.R | 1 + R/transform.R | 1 + R/unique.R | 1 + R/with.R | 1 + tests/testthat/testlaf.R | 7 ++++--- tests/testthat/testsave_ffdf.R |only 22 files changed, 80 insertions(+), 49 deletions(-)
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling
and multidimensional item response modeling for dichotomous
and polytomous data. This package enables the estimation of the
DINA and DINO model, the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic model (GDM),
the multidimensional linear compensatory item response model and
the structured latent class model (SLCA).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between CDM versions 4.2-12 dated 2015-02-23 and 4.3-0 dated 2015-06-05
CDM-4.2-12/CDM/R/gdm_temp.R |only CDM-4.3-0/CDM/DESCRIPTION | 10 +++--- CDM-4.3-0/CDM/MD5 | 25 ++++++++-------- CDM-4.3-0/CDM/NAMESPACE | 2 - CDM-4.3-0/CDM/R/IRT.jackknife.gdina.R | 2 + CDM-4.3-0/CDM/R/gdina.R | 25 ++++++++++------ CDM-4.3-0/CDM/R/summary.gdina.R | 9 ++++-- CDM-4.3-0/CDM/inst/NEWS | 12 +++++++- CDM-4.3-0/CDM/man/CDM-package.Rd | 51 ++++++++++++++++------------------ CDM-4.3-0/CDM/man/data.Students.Rd | 8 ++--- CDM-4.3-0/CDM/man/data.fraction1.Rd | 2 - CDM-4.3-0/CDM/man/data.mg.Rd | 2 - CDM-4.3-0/CDM/man/entropy.lca.Rd | 6 ++-- CDM-4.3-0/CDM/man/mcdina.Rd | 4 +- 14 files changed, 88 insertions(+), 70 deletions(-)
Title: The Skew-Normal and Skew-t Distributions
Description: Define and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and diagnostics, in the univariate and
the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.2-1 dated 2015-04-29 and 1.2-2 dated 2015-06-05
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 15 ++++++++++----- R/sn-funct.R | 43 ++++++++++++++++++++++++++++--------------- man/Qpenalty.Rd | 4 ++-- man/barolo.Rd | 10 ++++------ man/extractSECdistr.Rd | 2 +- man/selm.Rd | 18 ++++++++++-------- man/selm.fit.Rd | 15 ++++++++++----- 9 files changed, 77 insertions(+), 54 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Josh O'Brien [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.1-0 dated 2015-04-24 and 1.1-1 dated 2015-06-05
ChangeLog | 80 +++++++++++++++++++++++++++++++++++++ DESCRIPTION | 10 ++-- MD5 | 54 ++++++++++++------------ NAMESPACE | 8 +++ R/Spatial-methods.R | 22 ++++++---- R/SpatialGridDataFrame-methods.R | 6 -- R/SpatialPointsDataFrame-methods.R | 4 - R/bubble.R | 5 +- R/merge.R | 12 +++++ R/spdists.R | 58 ++++++++++++++++++++------ R/spplot.R | 67 +++++++++++++++--------------- inst/ChangeLog | 80 +++++++++++++++++++++++++++++++++++++ inst/doc/csdacm.pdf |binary inst/doc/intro_sp.pdf |binary inst/doc/over.pdf |binary inst/include/sp.h | 4 + man/Spatial-class.Rd | 2 man/SpatialLines.Rd | 7 +-- man/bubble.Rd | 6 ++ man/merge.Rd | 5 +- man/spDistsN1.Rd | 54 +++++++++++++++++++++++- src/gcdist.c | 31 ++++++++++---- src/init.c | 1 src/sp.h | 4 + src/zerodist.c | 2 tests/base.Rout.save | 27 +++++++++--- tests/grid.Rout.save | 16 +++++-- tests/pass1.Rout.save | 14 +++--- 28 files changed, 445 insertions(+), 134 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Tools for bivariate exploratory data analysis, bivariate copula selection and (vine) tree construction are provided. Vine copula models can be estimated either sequentially or by joint maximum likelihood estimation. Sampling algorithms and plotting methods are included. Data is assumed to lie in the unit hypercube (so-called copula data). For C- and D-vines links to the package 'CDVine' are provided.
Author: Ulf Schepsmeier, Jakob Stoeber, Eike Christian Brechmann, Benedikt Graeler, Thomas Nagler, Tobias Erhardt
Maintainer: Tobias Erhardt <tobias.erhardt@tum.de>
Diff between VineCopula versions 1.4 dated 2015-01-28 and 1.5 dated 2015-06-05
DESCRIPTION | 14 MD5 | 201 +-- NAMESPACE | 11 R/0_prep_object.R | 359 +++--- R/AD.R | 37 R/BetaMatrix.r | 65 - R/BiCop.R |only R/BiCopCDF.r | 325 +++-- R/BiCopChiPlot.r | 361 +++--- R/BiCopDeriv.r | 289 ++--- R/BiCopDeriv2.r | 364 +++--- R/BiCopEst.r | 1842 +++++++++++++++++---------------- R/BiCopGofTest.r | 1172 +++++++++++--------- R/BiCopHfunc.r | 226 ++-- R/BiCopHfuncDeriv.r | 192 +-- R/BiCopHfuncDeriv2.r | 251 ++-- R/BiCopIndTest.r | 34 R/BiCopLambda.r | 600 +++++----- R/BiCopMetaContour.r | 1389 ++++++++++++------------ R/BiCopName.r | 442 +++++-- R/BiCopPDF.r | 176 ++- R/BiCopPar2Beta.r | 106 + R/BiCopPar2TailDep.r | 310 +++-- R/BiCopPar2Tau.r | 605 ++++++---- R/BiCopSelect.r | 837 ++++++++------ R/BiCopSim.R | 187 ++- R/BiCopTau2Par.r | 101 - R/BiCopVuongClarke.r | 438 ++++--- R/C2RVine.r | 175 +-- R/ChatZj.R | 87 - R/CvM.R | 34 R/D2RVine.r | 173 +-- R/Fhat.R | 50 R/KS.R | 41 R/RVineAIC.r | 370 +++--- R/RVineClarkeTest.R | 80 - R/RVineCopSelect.r | 226 ++-- R/RVineGofTest3.r | 95 - R/RVineGrad.r | 211 +-- R/RVineHessian.r | 169 +-- R/RVineLogLik.r | 224 +--- R/RVineMLE.R | 876 ++++++++------- R/RVineMatrix.R | 940 +++++++++------- R/RVinePIT.r | 198 +-- R/RVinePar2Beta.r | 33 R/RVinePar2Tau.r | 33 R/RVinePartialcorr.R | 337 +++--- R/RVineSeqEst.R | 309 +++-- R/RVineSim.R | 134 +- R/RVineStdError.r | 128 +- R/RVineStructureSelect.r | 1136 ++++++++++---------- R/RVineTreePlot.r | 744 +++++++------ R/RVineVuongTest.R | 96 - R/TauMatrix.r | 93 - R/as.copuladata.R |only R/gof_ECP.r | 310 ++--- R/gof_PIT.r | 322 ++--- R/gof_White.r | 416 +++---- R/pairs.R |only R/plot.BiCop.R |only inst/ChangeLog | 27 man/BB8Copula.Rd | 8 man/BiCop.Rd |only man/BiCopCDF.Rd | 19 man/BiCopDeriv.Rd | 20 man/BiCopDeriv2.Rd | 21 man/BiCopEst.Rd | 6 man/BiCopGofTest.Rd | 12 man/BiCopHfunc.Rd | 12 man/BiCopHfuncDeriv.Rd | 22 man/BiCopHfuncDeriv2.Rd | 22 man/BiCopLambda.Rd | 31 man/BiCopMetaContour.Rd | 3 man/BiCopPDF.Rd | 19 man/BiCopPar2Beta.Rd | 10 man/BiCopPar2TailDep.Rd | 10 man/BiCopPar2Tau.Rd | 11 man/BiCopSelect.Rd | 8 man/BiCopSim.Rd | 9 man/BiCopVuongClarke.Rd | 7 man/RVineClarkeTest.Rd | 6 man/RVineCopSelect.Rd | 8 man/RVineCor2pcor.Rd | 94 - man/RVineGofTest.Rd | 11 man/RVineMLE.Rd | 8 man/RVineMatrix.Rd | 11 man/RVinePDF.Rd |only man/RVinePIT.Rd | 13 man/RVineStructureSelect.Rd | 12 man/RVineVuongTest.Rd | 4 man/VineCopula-package.Rd | 22 man/as.copuladata.Rd |only man/pairs.copuladata.Rd |only man/plot.BiCop.Rd |only man/vineCopula.Rd | 3 src/cdvine.c | 59 - src/deriv.c | 88 + src/deriv2.c | 51 src/evCopula.c | 70 + src/gof.c | 129 +- src/incompleteBeta.c | 9 src/logderiv.c | 22 src/pit.c | 29 src/rvinederiv.c | 73 - tests/Examples/VineCopula-Ex.Rout.save | 966 ++++++++++++++--- tests/additonalExampleRuns.Rout.save | 4 106 files changed, 11910 insertions(+), 9033 deletions(-)
Title: Robust Linear Mixed Effects Models
Description: Robust mixed effects modeling by robustification
of scoring equations using the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <koller.manuel@gmail.com>
Diff between robustlmm versions 1.6 dated 2014-07-11 and 1.7-2 dated 2015-06-05
robustlmm-1.6/robustlmm/R/zero.theta.R |only robustlmm-1.6/robustlmm/vignettes/cache |only robustlmm-1.7-2/robustlmm/DESCRIPTION | 10 robustlmm-1.7-2/robustlmm/MD5 | 70 +- robustlmm-1.7-2/robustlmm/NAMESPACE | 7 robustlmm-1.7-2/robustlmm/R/AllClass.R | 4 robustlmm-1.7-2/robustlmm/R/DAS-scale.R | 59 -- robustlmm-1.7-2/robustlmm/R/accessors.R | 16 robustlmm-1.7-2/robustlmm/R/fit.effects.R | 2 robustlmm-1.7-2/robustlmm/R/fromLme4.R | 10 robustlmm-1.7-2/robustlmm/R/helpers.R | 4 robustlmm-1.7-2/robustlmm/R/mutators.R | 11 robustlmm-1.7-2/robustlmm/R/rlmer.R | 2 robustlmm-1.7-2/robustlmm/inst/doc/rlmer.R | 237 -------- robustlmm-1.7-2/robustlmm/inst/doc/rlmer.Rnw | 291 ---------- robustlmm-1.7-2/robustlmm/inst/doc/rlmer.pdf |binary robustlmm-1.7-2/robustlmm/tests/compare-methods.Rout.save | 22 robustlmm-1.7-2/robustlmm/tests/getME.R | 3 robustlmm-1.7-2/robustlmm/tests/getME.Rout.save | 122 ++-- robustlmm-1.7-2/robustlmm/tests/tau.R | 9 robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-penicillin-qq-ranef.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-penicillin-qq-resid.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-penicillin-raw.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-penicillin-robustness-weights.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-penicillin-ta.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-ex-comparsion-subsample.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-ex-comparsion.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-qq-ranef.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-qq-resid.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-ranef-scatterplot.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-raw.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-sleepstudy-ta.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/figs/fig-ex-smoothedHuber.pdf |binary robustlmm-1.7-2/robustlmm/vignettes/rlmer.Rnw | 291 ---------- 34 files changed, 197 insertions(+), 973 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance proxies, such as mineralogical, petrographic or chemical compositions are compared with the Aitchison and Bray-Curtis distances.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 0.1 dated 2015-05-26 and 0.2 dated 2015-06-05
DESCRIPTION | 6 ++--- MD5 | 13 ++++++----- NAMESPACE | 1 R/provenance.R | 62 ++++++++++++++++++++++++++++----------------------------- man/dist.Rd | 3 ++ man/get.n.Rd |only man/get.p.Rd | 2 - man/getKDE.Rd | 3 -- 8 files changed, 47 insertions(+), 43 deletions(-)
Title: Support for Linear Models
Description: Accompanies Markus Brauer, Bas Rokers, and John Curtin's two-course graduate series in
General, Generalized, and Multi-level Linear Models (PSY 610/710).
Author: John Curtin <jjcurtin@wisc.edu>
Maintainer: John Curtin <jjcurtin@wisc.edu>
Diff between lmSupport versions 2.9.1 dated 2014-09-26 and 2.9.2 dated 2015-06-05
DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++----------- NAMESPACE | 3 ++- R/dfMerge.R | 39 +++++++++++++++++++++++++++++++++++---- R/dfReadDat.R | 6 +++--- R/dfRownames.R | 7 +++++-- R/modelCompare.R | 12 +++++++++--- R/modelPredictions.R | 2 +- R/varOdd.R |only man/dfMerge.Rd | 19 ++++++++++++------- man/dfReadDat.Rd | 5 +++-- man/dfRownames.Rd | 3 ++- man/modelCompare.Rd | 4 +--- man/varOdd.Rd |only 14 files changed, 90 insertions(+), 42 deletions(-)
Title: Isotope Pattern, Profile and Centroid Calculation for Mass
Spectrometry
Description: Fast and very memory-efficient calculation of isotope patterns,
subsequent convolution to theoretical envelopes (profiles) plus valley
detection and centroidization or intensoid calculation. Batch processing,
resolution interpolation, wrapper, adduct calculations and molecular
formula parsing.
Author: Martin Loos, Christian Gerber
Maintainer: Martin Loos <martin.loos@alumni.ethz.ch>
Diff between enviPat versions 1.9 dated 2014-07-14 and 2.0 dated 2015-06-05
enviPat-1.9/enviPat/src/n-tuple.c |only enviPat-1.9/enviPat/src/n-tuple.h |only enviPat-2.0/enviPat/DESCRIPTION | 17 enviPat-2.0/enviPat/MD5 | 62 enviPat-2.0/enviPat/NEWS | 7 enviPat-2.0/enviPat/R/envelope.R | 1 enviPat-2.0/enviPat/R/enviPat.R | 7 enviPat-2.0/enviPat/R/getR.R | 2 enviPat-2.0/enviPat/R/isopattern.R | 102 enviPat-2.0/enviPat/data/adducts.rda |binary enviPat-2.0/enviPat/data/isotopes.rda |binary enviPat-2.0/enviPat/data/resolution_list.rda |binary enviPat-2.0/enviPat/inst |only enviPat-2.0/enviPat/man/adducts.Rd | 16 enviPat-2.0/enviPat/man/envelope.Rd | 1 enviPat-2.0/enviPat/man/enviPat-package.Rd | 14 enviPat-2.0/enviPat/man/isopattern.Rd | 80 enviPat-2.0/enviPat/man/isotopes.Rd | 2 enviPat-2.0/enviPat/man/mergeform.Rd | 4 enviPat-2.0/enviPat/man/resolution_list.Rd | 12 enviPat-2.0/enviPat/man/vdetect.Rd | 1 enviPat-2.0/enviPat/src/combination.c | 3634 ++++++++++++++++++++------- enviPat-2.0/enviPat/src/combination.h | 317 +- enviPat-2.0/enviPat/src/data.h |only enviPat-2.0/enviPat/src/element.c | 13 enviPat-2.0/enviPat/src/element.h | 9 enviPat-2.0/enviPat/src/isotope.c | 20 enviPat-2.0/enviPat/src/isotope.h | 11 enviPat-2.0/enviPat/src/main.c | 3218 ++++++++++++++++++----- enviPat-2.0/enviPat/src/parse.c | 372 ++ enviPat-2.0/enviPat/src/parse.h | 52 enviPat-2.0/enviPat/src/preferences.h | 126 enviPat-2.0/enviPat/src/profile.c | 72 enviPat-2.0/enviPat/src/profile.h | 19 34 files changed, 6136 insertions(+), 2055 deletions(-)
Title: Colored Terminal Output
Description: Colored terminal output on
terminals that support ANSI color and highlight codes.
ANSI color support is automatically detected.
Colors and highlighting can be combined and nested. New styles
can also be created easily. This package was inspired by the chalk
JavaScript project.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between crayon versions 1.2.1 dated 2015-05-17 and 1.3.0 dated 2015-06-05
DESCRIPTION | 10 ++++---- MD5 | 48 ++++++++++++++++++++-------------------- NAMESPACE | 6 ++++- R/has_color.r | 8 +++++- R/parts.r |only R/utils.r | 13 ++++++++++ inst/NEWS.md | 8 ++++++ man/chr.Rd | 2 - man/col_nchar.Rd | 2 - man/col_strsplit.Rd | 2 - man/col_substr.Rd | 2 - man/col_substring.Rd | 2 - man/combine_styles.Rd | 2 - man/concat.Rd | 2 - man/crayon.Rd | 2 - man/drop_style.Rd | 2 - man/has_color.Rd | 2 - man/has_style.Rd | 2 - man/make_style.Rd | 2 - man/num_colors.Rd | 2 - man/show_ansi_colors.Rd | 2 - man/start.crayon.Rd |only man/strip_style.Rd | 2 - man/style.Rd | 2 - man/styles.Rd | 2 - tests/testthat/test-has-color.r | 31 +++++++++++++++++++++++++ 26 files changed, 110 insertions(+), 48 deletions(-)