Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes
of time series analysis and forecasting. The package includes Exponential Smoothing,
SARIMA, Complex Exponential Smoothing, Simple Moving Average, Vector Exponential
Smoothing in state space forms, several simulation functions and intermittent demand
state space models.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 2.4.7 dated 2018-12-02 and 2.5.0 dated 2019-04-25
smooth-2.4.7/smooth/R/error-measures.R |only smooth-2.4.7/smooth/man/Accuracy.Rd |only smooth-2.4.7/smooth/man/error-measures.Rd |only smooth-2.4.7/smooth/man/hm.Rd |only smooth-2.4.7/smooth/man/reexports.Rd |only smooth-2.4.7/smooth/src/ssgeneralfun.cpp |only smooth-2.4.7/smooth/tests/testthat/test_iss.R |only smooth-2.5.0/smooth/DESCRIPTION | 10 smooth-2.5.0/smooth/MD5 | 170 +++--- smooth-2.5.0/smooth/NAMESPACE | 42 - smooth-2.5.0/smooth/NEWS | 45 + smooth-2.5.0/smooth/R/RcppExports.R | 40 - smooth-2.5.0/smooth/R/autoces.R | 8 smooth-2.5.0/smooth/R/autogum.R | 27 - smooth-2.5.0/smooth/R/automsarima.R | 29 - smooth-2.5.0/smooth/R/autossarima.R | 28 - smooth-2.5.0/smooth/R/ces.R | 151 ++--- smooth-2.5.0/smooth/R/cma.R | 15 smooth-2.5.0/smooth/R/es.R | 342 ++++++------ smooth-2.5.0/smooth/R/gsi.R | 13 smooth-2.5.0/smooth/R/gum.R | 154 ++--- smooth-2.5.0/smooth/R/isFunctions.R | 14 smooth-2.5.0/smooth/R/iss.R | 164 ++---- smooth-2.5.0/smooth/R/methods.R | 136 +++-- smooth-2.5.0/smooth/R/msarima.R | 147 ++--- smooth-2.5.0/smooth/R/oes.R |only smooth-2.5.0/smooth/R/oesg.R |only smooth-2.5.0/smooth/R/simces.R | 4 smooth-2.5.0/smooth/R/simes.R | 9 smooth-2.5.0/smooth/R/simgum.R | 4 smooth-2.5.0/smooth/R/simsma.R | 2 smooth-2.5.0/smooth/R/simssarima.R | 9 smooth-2.5.0/smooth/R/sma.R | 15 smooth-2.5.0/smooth/R/smooth-package.R | 6 smooth-2.5.0/smooth/R/smoothCombine.R | 28 - smooth-2.5.0/smooth/R/ssarima.R | 156 ++--- smooth-2.5.0/smooth/R/ssfunctions.R | 692 +++++++++++++------------- smooth-2.5.0/smooth/R/ves.R | 23 smooth-2.5.0/smooth/R/vmethods.R | 20 smooth-2.5.0/smooth/R/vssFunctions.R | 47 + smooth-2.5.0/smooth/R/zzz.R | 4 smooth-2.5.0/smooth/README.md | 48 - smooth-2.5.0/smooth/build/partial.rdb |binary smooth-2.5.0/smooth/build/vignette.rds |binary smooth-2.5.0/smooth/inst/doc/ces.html | 390 +++++++++++--- smooth-2.5.0/smooth/inst/doc/es.html | 526 ++++++++++++++----- smooth-2.5.0/smooth/inst/doc/gum.R | 2 smooth-2.5.0/smooth/inst/doc/gum.Rmd | 2 smooth-2.5.0/smooth/inst/doc/gum.html | 403 +++++++++++---- smooth-2.5.0/smooth/inst/doc/oes.R |only smooth-2.5.0/smooth/inst/doc/oes.Rmd |only smooth-2.5.0/smooth/inst/doc/oes.html |only smooth-2.5.0/smooth/inst/doc/simulate.Rmd | 6 smooth-2.5.0/smooth/inst/doc/simulate.html | 537 ++++++++++++++------ smooth-2.5.0/smooth/inst/doc/sma.html | 331 ++++++++++-- smooth-2.5.0/smooth/inst/doc/smooth.Rmd | 7 smooth-2.5.0/smooth/inst/doc/smooth.html | 199 +++++++ smooth-2.5.0/smooth/inst/doc/ssarima.Rmd | 6 smooth-2.5.0/smooth/inst/doc/ssarima.html | 415 ++++++++++++--- smooth-2.5.0/smooth/inst/doc/ves.Rmd | 2 smooth-2.5.0/smooth/inst/doc/ves.html | 354 +++++++++++-- smooth-2.5.0/smooth/man/auto.ces.Rd | 46 - smooth-2.5.0/smooth/man/auto.gum.Rd | 46 - smooth-2.5.0/smooth/man/auto.msarima.Rd | 64 +- smooth-2.5.0/smooth/man/auto.ssarima.Rd | 65 +- smooth-2.5.0/smooth/man/ces.Rd | 61 +- smooth-2.5.0/smooth/man/es.Rd | 78 +- smooth-2.5.0/smooth/man/gum.Rd | 57 +- smooth-2.5.0/smooth/man/isFunctions.Rd | 8 smooth-2.5.0/smooth/man/iss.Rd | 9 smooth-2.5.0/smooth/man/msarima.Rd | 60 +- smooth-2.5.0/smooth/man/oes.Rd |only smooth-2.5.0/smooth/man/oesg.Rd |only smooth-2.5.0/smooth/man/sim.ces.Rd | 2 smooth-2.5.0/smooth/man/sim.es.Rd | 2 smooth-2.5.0/smooth/man/sim.gum.Rd | 2 smooth-2.5.0/smooth/man/sim.sma.Rd | 2 smooth-2.5.0/smooth/man/sim.ssarima.Rd | 10 smooth-2.5.0/smooth/man/smooth.Rd | 4 smooth-2.5.0/smooth/man/smoothCombine.Rd | 50 - smooth-2.5.0/smooth/man/ssarima.Rd | 67 +- smooth-2.5.0/smooth/man/ves.Rd | 59 +- smooth-2.5.0/smooth/src/RcppExports.cpp | 177 +++++- smooth-2.5.0/smooth/src/ssGeneral.cpp |only smooth-2.5.0/smooth/src/ssGeneral.h |only smooth-2.5.0/smooth/src/ssOccurrence.cpp |only smooth-2.5.0/smooth/src/ssSimulator.cpp |only smooth-2.5.0/smooth/tests/testthat/test_es.R | 2 smooth-2.5.0/smooth/tests/testthat/test_oes.R |only smooth-2.5.0/smooth/vignettes/gum.Rmd | 2 smooth-2.5.0/smooth/vignettes/library.bib | 48 + smooth-2.5.0/smooth/vignettes/oes.Rmd |only smooth-2.5.0/smooth/vignettes/simulate.Rmd | 6 smooth-2.5.0/smooth/vignettes/smooth.Rmd | 7 smooth-2.5.0/smooth/vignettes/ssarima.Rmd | 6 smooth-2.5.0/smooth/vignettes/ves.Rmd | 2 96 files changed, 4414 insertions(+), 2310 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 Müller [ctb],
Thomas Lin Pedersen [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.7-3 dated 2019-02-21 and 0.7-4 dated 2019-04-25
DESCRIPTION | 9 - MD5 | 137 +++++++++---------- NAMESPACE | 5 NEWS.md | 24 +++ R/arith.R | 7 R/crs.R | 15 +- R/geom.R | 55 ++++++- R/grid.R | 10 - R/init.R | 9 - R/maps.R | 2 R/plot.R | 4 R/sample.R | 6 R/sfc.R | 16 +- R/sgbp.R | 32 ++-- R/stars.R | 8 - R/tidyverse.R | 56 ++++--- R/transform.R | 6 build/vignette.rds |binary configure | 208 +++++++++++++++++++++++++++-- configure.ac | 138 +++++++++++++++++-- inst/CITATION | 13 + inst/doc/sf1.html | 104 +++++++++++--- inst/doc/sf2.html | 71 +++++++++- inst/doc/sf3.html | 65 +++++++++ inst/doc/sf4.html | 67 +++++++++ inst/doc/sf5.html | 67 +++++++++ inst/doc/sf6.html | 67 +++++++++ inst/docker/gdal/Dockerfile | 72 ++++++---- man/geos_binary_pred.Rd | 4 man/geos_measures.Rd | 8 - man/geos_unary.Rd | 13 + man/st_crs.Rd | 7 man/st_sample.Rd | 6 man/st_transform.Rd | 4 src/Makevars.win | 1 src/gdal.cpp | 30 ++++ src/gdal.h | 1 src/gdal_utils.cpp | 14 - src/gdal_write.cpp | 1 src/geos.cpp | 33 +++- src/ops.cpp | 10 - src/polygonize.cpp | 9 - src/proj.cpp | 281 +++++++++++++++------------------------- src/proj_info.cpp |only src/stars.cpp | 4 tests/crs.R | 1 tests/crs.Rout.save | 10 + tests/dist.R | 2 tests/dist.Rout.save | 8 - tests/dplyr.R | 2 tests/dplyr.Rout.save | 8 - tests/empty.R | 3 tests/empty.Rout.save | 9 - tests/gdal_geom.R | 4 tests/gdal_geom.Rout.save | 14 + tests/geos.R | 18 ++ tests/geos.Rout.save | 36 ++++- tests/grid.R | 1 tests/grid.Rout.save | 7 tests/roundtrip.R | 1 tests/roundtrip.Rout.save | 7 tests/sfc.R | 1 tests/sfc.Rout.save | 11 - tests/testthat.Rout.save | 10 - tests/testthat/test-normalize.R | 20 ++ tests/testthat/test_crs.R | 20 ++ tests/testthat/test_gdal.R | 1 tests/testthat/test_geos.R | 7 tests/units.R | 2 tests/units.Rout.save | 8 - 70 files changed, 1411 insertions(+), 499 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC)
and some related functions are implemented. Functions for incorporating
background knowledge are provided.
Author: Markus Kalisch [aut, cre],
Alain Hauser [aut],
Martin Maechler [aut],
Diego Colombo [ctb],
Doris Entner [ctb],
Patrik Hoyer [ctb],
Antti Hyttinen [ctb],
Jonas Peters [ctb],
Nicoletta Andri [ctb],
Emilija Perkovic [ctb],
Preetam Nandy [ctb],
Philipp Ruetimann [ctb],
Daniel Stekhoven [ctb],
Manuel Schuerch [ctb],
Marco Eigenmann [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.6-0 dated 2018-06-04 and 2.6-2 dated 2019-04-25
DESCRIPTION | 9 +- MD5 | 76 ++++++++++--------- R/gies.R | 9 +- R/jointIda.R | 2 R/pcalg.R | 126 +++++++++++++++++---------------- build/vignette.rds |binary inst/doc/pcalgDoc.R | 2 inst/doc/pcalgDoc.Rnw | 2 inst/doc/pcalgDoc.pdf |binary inst/doc/vignette2018.pdf |binary man/ages.Rd | 4 - man/backdoor.Rd | 1 man/dag2cpdag.Rd | 47 +++++------- man/ges.Rd | 3 man/ida.Rd | 1 man/pcSelect.Rd | 14 --- man/plotSG.Rd | 71 +++++++++++------- src/Makevars.win | 4 - tests/nohup.out |only tests/test_ages.R | 3 tests/test_backdoor.R | 23 +++--- tests/test_backdoor.Rout.save | 42 ++++++----- tests/test_causalEffect.R | 2 tests/test_displayAmat.R | 1 tests/test_fci.R | 4 - tests/test_gSquareBin.R | 1 tests/test_ida.R | 2 tests/test_idaFast.R | 2 tests/test_pcSelect.R | 2 tests/test_pcalg2dagitty.R | 3 tests/test_randDAG.R | 1 tests/test_randDAG.Rout.save | 9 +- tests/test_rfci.R | 3 tests/test_rmvDAG.R | 2 tests/test_shd.R | 2 tests/test_udag2pdag.R | 2 tests/test_wgtMatrix.R | 2 vignettes/auto |only vignettes/pcalgDoc-concordance.tex |only vignettes/pcalgDoc.Rnw | 2 vignettes/vignette2018-concordance.tex |only 41 files changed, 254 insertions(+), 225 deletions(-)
Title: Multinomial Processing Tree Models
Description: Fitting and testing multinomial processing tree (MPT) models, a
class of nonlinear models for categorical data. The parameters are the
link probabilities of a tree-like graph and represent the latent cognitive
processing steps executed to arrive at observable response categories
(Batchelder & Riefer, 1999 <doi:10.3758/bf03210812>; Erdfelder et al., 2009
<doi:10.1027/0044-3409.217.3.108>; Riefer & Batchelder, 1988
<doi:10.1037/0033-295x.95.3.318>).
Author: Florian Wickelmaier [aut, cre],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Florian Wickelmaier <wickelmaier@web.de>
Diff between mpt versions 0.5-4 dated 2016-09-08 and 0.6-0 dated 2019-04-25
ChangeLog | 11 ++++++ DESCRIPTION | 18 +++++----- MD5 | 46 +++++++++++++------------ R/mpt.R | 4 ++ R/mptspec.R | 38 ++++++++++++++++++++- build/partial.rdb |binary data/proact.rda |binary data/prospecMemory.rda |binary data/recogROC.rda |binary data/retroact.rda |binary data/selectiontask.rda |only man/citysize.Rd | 4 +- man/logLik.mpt.Rd | 22 +++++++----- man/mpt.Rd | 20 +++++------ man/mptEM.Rd | 3 - man/mptspec.Rd | 19 +++++++--- man/plot.mpt.Rd | 17 ++++----- man/proact.Rd | 23 ++++++------ man/prospecMemory.Rd | 88 +++++++++++++++++++++++++++++++++++++------------ man/recogROC.Rd | 28 +++++++++------ man/retroact.Rd | 51 +++++++++++++++------------- man/selectiontask.Rd |only man/simulate.mpt.Rd | 12 +++--- man/valence.Rd | 15 +++++--- man/vcov.mpt.Rd | 16 ++------ 25 files changed, 275 insertions(+), 160 deletions(-)
Title: Data-Driven Plot Design
Description: Designs plots in terms of core structure. See 'example(metaplot)'.
Primary arguments are (unquoted) column names; order and type (numeric or not)
dictate the resulting plot. Specify any y variables, x variable, any groups variable,
and any conditioning variables to metaplot() to generate density plots, boxplots,
mosaic plots, scatterplots, scatterplot matrices, or conditioned plots. Use multiplot()
to arrange plots in grids. Wherever present, scalar column attributes 'label' and 'guide'
are honored, producing fully annotated plots with minimal effort. Attribute 'guide'
is typically units, but may be encoded() to provide interpretations of categorical
values (see '?encode'). Utility unpack() transforms scalar column attributes to row
values and pack() does the reverse, supporting tool-neutral storage of metadata along
with primary data. The package supports customizable aesthetics such as such as reference
lines, unity lines, smooths, log transformation, and linear fits. The user may choose
between trellis and ggplot output. Compact syntax and integrated metadata promote workflow
scalability.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between metaplot versions 0.8.2 dated 2019-02-04 and 0.8.3 dated 2019-04-25
metaplot-0.8.2/metaplot/man/as_factor.Rd |only metaplot-0.8.3/metaplot/DESCRIPTION | 8 ++--- metaplot-0.8.3/metaplot/MD5 | 7 +--- metaplot-0.8.3/metaplot/NAMESPACE | 1 metaplot-0.8.3/metaplot/R/utils.R | 48 ------------------------------- 5 files changed, 8 insertions(+), 56 deletions(-)
Title: An Implementation of Parametric and Nonparametric Event Study
Description: An implementation of a most commonly used event study methodology,
including both parametric and nonparametric tests. It contains variety
aspects of the rate of return estimation (the core calculation is done in
C++), as well as three classical for event study market models: mean
adjusted returns, market adjusted returns and single-index market models.
There are 6 parametric and 6 nonparametric tests provided, which examine
cross-sectional daily abnormal return (see the documentation of the
functions for more information). Parametric tests include tests proposed by
Brown and Warner (1980) <DOI:10.1016/0304-405X(80)90002-1>, Brown and Warner
(1985) <DOI:10.1016/0304-405X(85)90042-X>, Boehmer et al. (1991)
<DOI:10.1016/0304-405X(91)90032-F>, Patell (1976) <DOI:10.2307/2490543>, and
Lamb (1995) <DOI:10.2307/253695>. Nonparametric tests covered in estudy2 are
tests described in Corrado and Zivney (1992) <DOI:10.2307/2331331>,
McConnell and Muscarella (1985) <DOI:10.1016/0304-405X(85)90006-6>,
Boehmer et al. (1991) <DOI:10.1016/0304-405X(91)90032-F>, Cowan (1992)
<DOI:10.1007/BF00939016>, Corrado (1989) <DOI:10.1016/0304-405X(89)90064-0>,
Campbell and Wasley (1993) <DOI:10.1016/0304-405X(93)90025-7>, Savickas (2003)
<DOI:10.1111/1475-6803.00052>, Kolari and Pynnonen (2010)
<DOI:10.1093/rfs/hhq072>. Furthermore, tests for the cumulative
abnormal returns proposed by Brown and Warner (1985)
<DOI:10.1016/0304-405X(85)90042-X> and Lamb (1995) <DOI:10.2307/253695>
are included.
Author: Iegor Rudnytskyi [aut, cre]
Maintainer: Iegor Rudnytskyi <iegor.rudnytskyi@gmail.com>
Diff between estudy2 versions 0.8.5 dated 2018-07-03 and 0.9.0 dated 2019-04-25
DESCRIPTION | 15 ++--- MD5 | 61 ++++++++++---------- NAMESPACE | 2 NEWS.md | 9 +++ R/apply_market_model.R | 30 ++++++++++ R/car_nonparametric_tests.R |only R/car_parametric_tests.R | 108 ++++++++++++++++++++++++++---------- R/nonparametric_tests.R | 69 +++++++++++++++++++++-- R/parametric_tests.R | 116 +++++++++++++++++++++++++++------------ README.md | 26 +++++++- build/vignette.rds |binary inst/doc/estudy2-intro.html | 121 ++++++++++++++++++++++++++--------------- man/boehmer.Rd | 11 +++ man/brown_warner_1980.Rd | 11 +++ man/brown_warner_1985.Rd | 29 ++++++--- man/car_brown_warner_1985.Rd | 27 ++++++--- man/car_lamb.Rd | 15 ++++- man/car_nonparametric_tests.Rd |only man/car_parametric_tests.Rd | 17 ++++- man/car_rank_test.Rd |only man/corrado_sign_test.Rd | 10 +++ man/generalized_sign_test.Rd | 10 +++ man/get_rates_from_prices.Rd | 4 - man/lamb.Rd | 11 +++ man/modified_rank_test.Rd | 10 +++ man/nonparametric_tests.Rd | 9 ++- man/parametric_tests.Rd | 13 +++- man/patell.Rd | 11 +++ man/rank_test.Rd | 10 +++ man/returns.Rd | 4 - man/sign_test.Rd | 10 +++ man/t_test.Rd | 11 +++ man/wilcoxon_test.Rd | 10 +++ 33 files changed, 590 insertions(+), 200 deletions(-)
Title: Accessing the 'CHILDES' Database
Description: Tools for connecting to 'CHILDES', an open repository for
transcripts of parent-child interaction. For more information on the
underlying data, see <http://childes-db.stanford.edu>.
Author: Mika Braginsky [aut, cre],
Alessandro Sanchez [aut, ctb],
Daniel Yurovsky [aut],
Kyle MacDonald [ctb],
Stephan Meylan [ctb]
Maintainer: Mika Braginsky <mika.br@gmail.com>
Diff between childesr versions 0.1.0 dated 2018-05-18 and 0.1.1 dated 2019-04-25
DESCRIPTION | 8 MD5 | 21 - NEWS.md |only R/childesr.R | 4 inst/doc/access_childes_db.html | 509 +++++++++++++++++++++++++++++----------- man/get_collections.Rd | 3 man/get_contexts.Rd | 5 man/get_corpora.Rd | 3 man/get_participants.Rd | 7 man/get_speaker_statistics.Rd | 5 man/get_tokens.Rd | 7 man/get_transcripts.Rd | 5 12 files changed, 410 insertions(+), 167 deletions(-)
Title: Machine Learning in R
Description: Interface to a large number of classification and
regression techniques, including machine-readable parameter
descriptions. There is also an experimental extension for survival
analysis, clustering and general, example-specific cost-sensitive
learning. Generic resampling, including cross-validation,
bootstrapping and subsampling. Hyperparameter tuning with modern
optimization techniques, for single- and multi-objective problems.
Filter and wrapper methods for feature selection. Extension of basic
learners with additional operations common in machine learning, also
allowing for easy nested resampling. Most operations can be
parallelized.
Author: Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Lars Kotthoff [aut],
Julia Schiffner [aut],
Jakob Richter [aut],
Zachary Jones [aut],
Giuseppe Casalicchio [aut] (<https://orcid.org/0000-0001-5324-5966>),
Mason Gallo [aut],
Patrick Schratz [aut, cre] (<https://orcid.org/0000-0003-0748-6624>),
Jakob Bossek [ctb] (<https://orcid.org/0000-0002-4121-4668>),
Erich Studerus [ctb] (<https://orcid.org/0000-0003-4233-0182>),
Leonard Judt [ctb],
Tobias Kuehn [ctb],
Pascal Kerschke [ctb] (<https://orcid.org/0000-0003-2862-1418>),
Florian Fendt [ctb],
Philipp Probst [ctb] (<https://orcid.org/0000-0001-8402-6790>),
Xudong Sun [ctb] (<https://orcid.org/0000-0003-3269-2307>),
Janek Thomas [ctb] (<https://orcid.org/0000-0003-4511-6245>),
Bruno Vieira [ctb],
Laura Beggel [ctb] (<https://orcid.org/0000-0002-8872-8535>),
Quay Au [ctb] (<https://orcid.org/0000-0002-5252-8902>),
Martin Binder [ctb],
Florian Pfisterer [ctb],
Stefan Coors [ctb],
Steve Bronder [ctb],
Alexander Engelhardt [ctb],
Christoph Molnar [ctb]
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr versions 2.13 dated 2018-08-28 and 2.14.0 dated 2019-04-25
mlr-2.13/mlr/man/getFilterValues.Rd |only mlr-2.13/mlr/tests/testthat/Rplots.pdf |only mlr-2.14.0/mlr/DESCRIPTION | 220 ++- mlr-2.14.0/mlr/MD5 | 290 ++--- mlr-2.14.0/mlr/NAMESPACE | 13 mlr-2.14.0/mlr/NEWS |only mlr-2.14.0/mlr/NEWS.md | 69 + mlr-2.14.0/mlr/R/BaseWrapper.R | 5 mlr-2.14.0/mlr/R/ClassifTask.R | 6 mlr-2.14.0/mlr/R/ClusterTask.R | 6 mlr-2.14.0/mlr/R/CostSensTask.R | 8 mlr-2.14.0/mlr/R/FeatSelResult.R | 30 mlr-2.14.0/mlr/R/Filter.R | 566 +++++++++- mlr-2.14.0/mlr/R/FilterWrapper.R | 35 mlr-2.14.0/mlr/R/Learner.R | 5 mlr-2.14.0/mlr/R/ModelMultiplexer.R | 5 mlr-2.14.0/mlr/R/MultilabelTask.R | 14 mlr-2.14.0/mlr/R/RLearner.R | 2 mlr-2.14.0/mlr/R/RLearner_classif_h2odeeplearning.R | 8 mlr-2.14.0/mlr/R/RLearner_classif_h2ogbm.R | 9 mlr-2.14.0/mlr/R/RLearner_classif_h2oglm.R | 16 mlr-2.14.0/mlr/R/RLearner_classif_h2orandomForest.R | 15 mlr-2.14.0/mlr/R/RLearner_classif_liquidSVM.R |only mlr-2.14.0/mlr/R/RLearner_regr_h2ogbm.R | 52 mlr-2.14.0/mlr/R/RLearner_regr_liquidSVM.R |only mlr-2.14.0/mlr/R/RLearner_surv_ranger.R | 2 mlr-2.14.0/mlr/R/RegrTask.R | 6 mlr-2.14.0/mlr/R/ResampleDesc.R | 26 mlr-2.14.0/mlr/R/ResampleInstance.R | 14 mlr-2.14.0/mlr/R/ResampleInstances.R | 62 + mlr-2.14.0/mlr/R/SurvTask.R | 6 mlr-2.14.0/mlr/R/Task.R | 20 mlr-2.14.0/mlr/R/Task_operators.R | 2 mlr-2.14.0/mlr/R/TuneWrapper.R | 11 mlr-2.14.0/mlr/R/WeightedClassesWrapper.R | 3 mlr-2.14.0/mlr/R/cache_helpers.R |only mlr-2.14.0/mlr/R/createSpatialResamplingPlots.R | 32 mlr-2.14.0/mlr/R/filterFeatures.R | 47 mlr-2.14.0/mlr/R/generateFilterValues.R | 50 mlr-2.14.0/mlr/R/generateHyperParsEffect.R | 2 mlr-2.14.0/mlr/R/getFeatureImportance.R | 2 mlr-2.14.0/mlr/R/getResamplingIndices.R | 17 mlr-2.14.0/mlr/R/learners.R | 2 mlr-2.14.0/mlr/R/measures.R | 6 mlr-2.14.0/mlr/R/performance.R | 46 mlr-2.14.0/mlr/R/plotBMRRanksAsBarChart.R | 2 mlr-2.14.0/mlr/R/plotLearnerPrediction.R | 6 mlr-2.14.0/mlr/R/selectFeatures.R | 24 mlr-2.14.0/mlr/R/selectFeaturesExhaustive.R | 2 mlr-2.14.0/mlr/R/selectFeaturesGA.R | 2 mlr-2.14.0/mlr/R/selectFeaturesRandom.R | 2 mlr-2.14.0/mlr/R/selectFeaturesSequential.R | 3 mlr-2.14.0/mlr/R/setThreshold.R | 4 mlr-2.14.0/mlr/R/tuneIrace.R | 2 mlr-2.14.0/mlr/R/tuneParams.R | 26 mlr-2.14.0/mlr/R/tuneThreshold.R | 22 mlr-2.14.0/mlr/R/utils.R | 6 mlr-2.14.0/mlr/R/utils_opt.R | 16 mlr-2.14.0/mlr/build/vignette.rds |binary mlr-2.14.0/mlr/inst/doc/mlr.Rmd | 2 mlr-2.14.0/mlr/inst/doc/mlr.html | 189 +++ mlr-2.14.0/mlr/man/ClassifTask.Rd |only mlr-2.14.0/mlr/man/ClusterTask.Rd |only mlr-2.14.0/mlr/man/CostSensTask.Rd |only mlr-2.14.0/mlr/man/MultilabelTask.Rd |only mlr-2.14.0/mlr/man/RLearner.Rd | 2 mlr-2.14.0/mlr/man/RegrTask.Rd |only mlr-2.14.0/mlr/man/SurvTask.Rd |only mlr-2.14.0/mlr/man/Task.Rd | 93 - mlr-2.14.0/mlr/man/cache_helpers.Rd |only mlr-2.14.0/mlr/man/figures |only mlr-2.14.0/mlr/man/filterFeatures.Rd | 26 mlr-2.14.0/mlr/man/generateCalibrationData.Rd | 1 mlr-2.14.0/mlr/man/generateCritDifferencesData.Rd | 1 mlr-2.14.0/mlr/man/generateFeatureImportanceData.Rd | 1 mlr-2.14.0/mlr/man/generateFilterValuesData.Rd | 6 mlr-2.14.0/mlr/man/generateLearningCurveData.Rd | 1 mlr-2.14.0/mlr/man/generatePartialDependenceData.Rd | 1 mlr-2.14.0/mlr/man/generateThreshVsPerfData.Rd | 1 mlr-2.14.0/mlr/man/getFeatureImportance.Rd | 2 mlr-2.14.0/mlr/man/getFilteredFeatures.Rd | 1 mlr-2.14.0/mlr/man/getTaskCosts.Rd | 2 mlr-2.14.0/mlr/man/learners.Rd | 2 mlr-2.14.0/mlr/man/listFilterMethods.Rd | 1 mlr-2.14.0/mlr/man/makeBaseWrapper.Rd | 2 mlr-2.14.0/mlr/man/makeCostSensClassifWrapper.Rd | 4 mlr-2.14.0/mlr/man/makeCostSensRegrWrapper.Rd | 4 mlr-2.14.0/mlr/man/makeCostSensWeightedPairsWrapper.Rd | 6 mlr-2.14.0/mlr/man/makeFeatSelWrapper.Rd | 6 mlr-2.14.0/mlr/man/makeFilter.Rd | 13 mlr-2.14.0/mlr/man/makeFilterWrapper.Rd | 22 mlr-2.14.0/mlr/man/makeMeasure.Rd | 2 mlr-2.14.0/mlr/man/makeModelMultiplexer.Rd | 5 mlr-2.14.0/mlr/man/makeResampleDesc.Rd | 15 mlr-2.14.0/mlr/man/makeResampleInstance.Rd | 2 mlr-2.14.0/mlr/man/makeWeightedClassesWrapper.Rd | 3 mlr-2.14.0/mlr/man/measures.Rd | 4 mlr-2.14.0/mlr/man/mlr-package.Rd | 26 mlr-2.14.0/mlr/man/performance.Rd | 6 mlr-2.14.0/mlr/man/plotFilterValues.Rd | 4 mlr-2.14.0/mlr/man/selectFeatures.Rd | 6 mlr-2.14.0/mlr/man/tuneParams.Rd | 19 mlr-2.14.0/mlr/man/tuneThreshold.Rd | 6 mlr-2.14.0/mlr/src/Makevars.win |only mlr-2.14.0/mlr/tests/run-base.R | 2 mlr-2.14.0/mlr/tests/run-basenocran.R | 2 mlr-2.14.0/mlr/tests/run-classif1.R | 3 mlr-2.14.0/mlr/tests/run-classif2.R | 2 mlr-2.14.0/mlr/tests/run-cluster.R | 3 mlr-2.14.0/mlr/tests/run-featsel.R | 2 mlr-2.14.0/mlr/tests/run-learners-classif.R | 2 mlr-2.14.0/mlr/tests/run-learners-classiflabelswitch.R | 2 mlr-2.14.0/mlr/tests/run-learners-cluster.R | 2 mlr-2.14.0/mlr/tests/run-learners-general.R | 2 mlr-2.14.0/mlr/tests/run-learners-multilabel.R | 2 mlr-2.14.0/mlr/tests/run-learners-regr.R | 2 mlr-2.14.0/mlr/tests/run-learners-surv.R | 2 mlr-2.14.0/mlr/tests/run-multilabel.R | 2 mlr-2.14.0/mlr/tests/run-regr.R | 2 mlr-2.14.0/mlr/tests/run-stack.R | 2 mlr-2.14.0/mlr/tests/run-surv.R | 2 mlr-2.14.0/mlr/tests/run-tune.R | 2 mlr-2.14.0/mlr/tests/testthat/test_base_BaseEnsemble.R | 2 mlr-2.14.0/mlr/tests/testthat/test_base_Learner.R | 2 mlr-2.14.0/mlr/tests/testthat/test_base_TuneWrapper.R | 31 mlr-2.14.0/mlr/tests/testthat/test_base_blocking.R | 6 mlr-2.14.0/mlr/tests/testthat/test_base_caching.R |only mlr-2.14.0/mlr/tests/testthat/test_base_createDummyFeatures.R | 7 mlr-2.14.0/mlr/tests/testthat/test_base_fixed_indices_cv.R |only mlr-2.14.0/mlr/tests/testthat/test_base_generateFilterValuesData.R | 6 mlr-2.14.0/mlr/tests/testthat/test_base_generateHyperParsEffect.R | 2 mlr-2.14.0/mlr/tests/testthat/test_base_getFeatureImportance.R | 2 mlr-2.14.0/mlr/tests/testthat/test_base_getOOBPreds.R | 2 mlr-2.14.0/mlr/tests/testthat/test_base_resample_getResamplingIndices.R | 25 mlr-2.14.0/mlr/tests/testthat/test_base_selectFeatures.R | 8 mlr-2.14.0/mlr/tests/testthat/test_base_tuneThreshold.R |only mlr-2.14.0/mlr/tests/testthat/test_classif_h2odeeplearning.R | 16 mlr-2.14.0/mlr/tests/testthat/test_classif_h2ogbm.R | 16 mlr-2.14.0/mlr/tests/testthat/test_classif_h2oglm.R | 16 mlr-2.14.0/mlr/tests/testthat/test_classif_h2orandomForest.R | 16 mlr-2.14.0/mlr/tests/testthat/test_classif_liquidSVM.R |only mlr-2.14.0/mlr/tests/testthat/test_featsel_FeatSelWrapper.R | 22 mlr-2.14.0/mlr/tests/testthat/test_featsel_FilterWrapper.R | 7 mlr-2.14.0/mlr/tests/testthat/test_featsel_filters.R | 9 mlr-2.14.0/mlr/tests/testthat/test_featsel_fselectorrcpp.R |only mlr-2.14.0/mlr/tests/testthat/test_featsel_praznik.R |only mlr-2.14.0/mlr/tests/testthat/test_featsel_selectFeaturesSequential.R |only mlr-2.14.0/mlr/tests/testthat/test_regr_h2ogbm.R | 25 mlr-2.14.0/mlr/tests/testthat/test_regr_laGP.R | 2 mlr-2.14.0/mlr/tests/testthat/test_regr_liquidSVM.R |only mlr-2.14.0/mlr/tests/testthat/test_regr_ranger.R | 10 mlr-2.14.0/mlr/tests/testthat/test_tuneParams.R | 2 mlr-2.14.0/mlr/tests/testthat/test_tune_tuneIrace.R | 2 mlr-2.14.0/mlr/vignettes/mlr.Rmd | 2 154 files changed, 1982 insertions(+), 628 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; supports sf and stars.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 2.0-0 dated 2019-02-28 and 2.0-1 dated 2019-04-25
DESCRIPTION | 21 +++++++----- MD5 | 57 +++++++++++++++++------------------ NEWS.md |only R/krige.R | 19 +++++++---- R/krigeST.R | 14 +++++++- build/vignette.rds |binary data/DE_RB_2005.rda |binary 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 inst/doc/gstat.pdf |binary inst/doc/prs.pdf |binary inst/doc/spatio-temporal-kriging.pdf |binary inst/doc/st.pdf |binary man/image.Rd | 11 ------ man/wind.Rd | 4 ++ tests/stars.R | 2 - tests/stars.Rout.save | 32 +++++++++---------- tests/windst.Rout.save | 16 +++++++-- 30 files changed, 99 insertions(+), 77 deletions(-)
Title: Propensity to Cycle Tool
Description: Functions and example data to teach and
increase the reproducibility of the methods and code underlying
the Propensity to Cycle Tool (PCT), a research project and web application
hosted at <https://www.pct.bike/>.
For an academic paper on the methods,
see Lovelace et al (2017) <doi:10.5198/jtlu.2016.862>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between pct versions 0.1.2 dated 2019-04-16 and 0.1.3 dated 2019-04-25
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/get_pct.R | 4 ++++ inst/doc/pct-international.html | 30 +++++++++++++++--------------- inst/doc/pct.html | 26 +++++++++++++------------- 6 files changed, 44 insertions(+), 36 deletions(-)
Title: Regression Models for Ordinal Data
Description: Implementation of cumulative link (mixed) models also known
as ordered regression models, proportional odds models, proportional
hazards models for grouped survival times and ordered logit/probit/...
models. Estimation is via maximum likelihood and mixed models are fitted
with the Laplace approximation and adaptive Gauss-Hermite quadrature.
Multiple random effect terms are allowed and they may be nested, crossed or
partially nested/crossed. Restrictions of symmetry and equidistance can be
imposed on the thresholds (cut-points/intercepts). Standard model
methods are available (summary, anova, drop-methods, step,
confint, predict etc.) in addition to profile methods and slice
methods for visualizing the likelihood function and checking
convergence.
Author: Rune Haubo Bojesen Christensen [aut, cre]
Maintainer: Rune Haubo Bojesen Christensen <rune.haubo@gmail.com>
Diff between ordinal versions 2019.3-9 dated 2019-03-09 and 2019.4-25 dated 2019-04-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 4 ++++ R/clm.frames.R | 17 ++++++++--------- R/clmm.R | 9 +++++---- build/vignette.rds |binary inst/doc/clm_article.pdf |binary inst/doc/clmm2_tutorial.pdf |binary 8 files changed, 28 insertions(+), 24 deletions(-)
Title: Identification of Periodically Expressed Genes
Description: The GeneCycle package implements the approaches of Wichert
et al. (2004) <doi.org/10.1093/bioinformatics/btg364>, Ahdesmaki
et al. (2005) <DOI:10.1186/1471-2105-6-117> and Ahdesmaki et al.
(2007) <DOI:10.1186/1471-2105-8-233> for detecting periodically
expressed genes from gene expression time series data.
Author: Miika Ahdesmaki, Konstantinos Fokianos, and Korbinian Strimmer.
Maintainer: Miika Ahdesmaki <miika.ahdesmaki@gmail.com>
Diff between GeneCycle versions 1.1.3 dated 2019-04-18 and 1.1.4 dated 2019-04-25
CHANGES | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/robust.spectrum.R | 43 ++++++++++++++++++++++++++----------------- 4 files changed, 36 insertions(+), 24 deletions(-)
Title: Customizable Object Sensitive Messages
Description: Messages should provide users with readable information
about R objects without flooding their console.
'cc()' concatenates vector and data frame values
into a grammatically correct string using commas, an ellipsis and conjunction.
'cn()' allows the user to define a string which varies based on a count.
'co()' combines the two to produce a customizable object aware string.
The package further facilitates this process by providing five 'sprintf'-like
types such as '%n' for the length of an object and '%o' for its name as
well as wrappers for pasting objects and issuing errors, warnings and messages.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
James Dunham [aut]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between err versions 0.0.1 dated 2018-10-28 and 0.2.0 dated 2019-04-25
err-0.0.1/err/R/err.R |only err-0.0.1/err/tests/testthat/test-err.R |only err-0.2.0/err/DESCRIPTION | 9 ++---- err-0.2.0/err/MD5 | 24 +++++++++-------- err-0.2.0/err/NAMESPACE | 4 ++ err-0.2.0/err/NEWS.md | 5 +++ err-0.2.0/err/R/utils.R | 28 ++++++++++++++++++++ err-0.2.0/err/R/wrappers.R |only err-0.2.0/err/README.md | 37 +++++++++------------------ err-0.2.0/err/man/err.Rd | 2 - err-0.2.0/err/man/err_wrappers.Rd |only err-0.2.0/err/man/figures |only err-0.2.0/err/man/msg.Rd | 2 - err-0.2.0/err/man/wrn.Rd | 2 - err-0.2.0/err/tests/testthat/test-utils.R | 16 +++++++++++ err-0.2.0/err/tests/testthat/test-wrappers.R |only 16 files changed, 86 insertions(+), 43 deletions(-)
Title: Analysis of Simulation Studies Including Monte Carlo Error
Description: Summarise results from simulation studies and compute Monte Carlo
standard errors of commonly used summary statistics. This package is modelled
on the 'simsum' user-written command in 'Stata' (See White I.R., 2010
<http://www.stata-journal.com/article.html?article=st0200>).
Author: Alessandro Gasparini [aut, cre]
(<https://orcid.org/0000-0002-8319-7624>),
Ian R. White [aut]
Maintainer: Alessandro Gasparini <ag475@leicester.ac.uk>
Diff between rsimsum versions 0.5.1 dated 2019-03-15 and 0.5.2 dated 2019-04-25
rsimsum-0.5.1/rsimsum/man/figures/README-bar-1.png |only rsimsum-0.5.1/rsimsum/man/figures/README-forest-1.png |only rsimsum-0.5.1/rsimsum/man/figures/README-pattern-1.png |only rsimsum-0.5.2/rsimsum/DESCRIPTION | 6 +-- rsimsum-0.5.2/rsimsum/MD5 | 29 ++++++--------- rsimsum-0.5.2/rsimsum/NEWS.md | 6 +++ rsimsum-0.5.2/rsimsum/R/plot-types.R | 4 +- rsimsum-0.5.2/rsimsum/README.md | 15 +++---- rsimsum-0.5.2/rsimsum/build/partial.rdb |binary rsimsum-0.5.2/rsimsum/inst/doc/introduction.html | 4 +- rsimsum-0.5.2/rsimsum/inst/doc/plotting.html | 12 +++--- rsimsum-0.5.2/rsimsum/inst/doc/relhaz.html | 4 +- rsimsum-0.5.2/rsimsum/inst/doc/rsimsumtidyverse.html | 4 +- rsimsum-0.5.2/rsimsum/man/figures/README-ba-1.png |binary rsimsum-0.5.2/rsimsum/man/figures/README-lolly-1.png |binary rsimsum-0.5.2/rsimsum/man/figures/README-ridgeline-1.png |binary rsimsum-0.5.2/rsimsum/man/figures/README-zipper-1.png |binary 17 files changed, 43 insertions(+), 41 deletions(-)
Title: Simulating and Conducting Phase 123 Trials
Description: Contains three simulation functions for implementing the entire Phase 123 trial and the separate Eff-Tox and Phase 3 portions of the trial, which may be beneficial for use on clusters. The functions AssignEffTox() and RandomizeEffTox() assign doses to patient cohorts during phase 12 and Reoptimize() determines the optimal dose to continue with during Phase 3. The functions ReturnMeansAgent() and ReturnMeanControl() gives the true mean survival for the agent doses and control and ReturnOCS() gives the operating characteristics of the design.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <achapp@lsuhsc.edu>
Diff between Phase123 versions 2.0 dated 2018-11-09 and 2.1 dated 2019-04-25
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/PHASE123CODE.cpp | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis
of chemical toxicokinetics ("TK") as in Pearce et al. (2017)
<doi:10.18637/jss.v079.i04>. Chemical-specific in vitro
data have been obtained from relatively high throughput
experiments. Both physiologically-based ("PBTK") and empirical
(e.g., one compartment) "TK" models can be parameterized for
several hundred chemicals and multiple species. These models are
solved efficiently, often using compiled (C-based) code. A Monte
Carlo sampler is included for simulating biological variability
(Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>)
and measurement limitations. Calibrated methods are included for
predicting tissue:plasma partition coefficients and volume of
distribution
(Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>).
These functions and data provide a set of tools for
in vitro-in vivo extrapolation ("IVIVE") of high throughput
screening data (e.g., Tox21, ToxCast) to real-world exposures via
reverse dosimetry (also known as "RTK")
(Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).
Author: John Wambaugh [aut, cre],
Robert Pearce [aut],
Caroline Ring [aut],
Greg Honda [aut],
Jimena Davis [ctb],
Nisha Sipes [ctb],
Barbara Wetmore [ctb],
Woodrow Setzer [ctb]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 1.9.1 dated 2019-04-17 and 1.9.2 dated 2019-04-25
DESCRIPTION | 8 MD5 | 78 ++-- NEWS |binary R/Parameterize_SteadyState.R | 3 R/calc_analytic_css.R | 4 R/calc_mc_css.R | 49 +-- R/convert_httk.R | 19 + R/draw_fup_clint.R | 6 R/get_cheminfo.R | 4 R/modelinfo_3compss.R | 1 build/partial.rdb |binary inst/doc/Pearce_2017_partitioning_plots.html | 4 inst/doc/Ring_2017_supplemental_vignette_age_dist.html | 4 inst/doc/Ring_2017_supplemental_vignette_globalsensitivityanalysis.html | 4 inst/doc/Ring_2017_supplemental_vignette_globalsensitivityplot.html | 4 inst/doc/Ring_2017_supplemental_vignette_heightweight_splines_kde.html | 4 inst/doc/Ring_2017_supplemental_vignette_hematocrit_splines.html | 4 inst/doc/Ring_2017_supplemental_vignette_plot_css95.html | 4 inst/doc/Ring_2017_supplemental_vignette_serumcreat_splines_kde.html | 4 inst/doc/Ring_2017_vignette01_subpopulations.html | 4 inst/doc/Ring_2017_vignette02_evalmodelsubpop.html | 4 inst/doc/Ring_2017_vignette03_paper_fig2.html | 4 inst/doc/Ring_2017_vignette04_paper_fig3.html | 4 inst/doc/Ring_2017_vignette05b_plothowgatejohnson.html | 4 inst/doc/Ring_2017_vignette06_aerplotting.html | 4 inst/doc/Ring_2017_vignette_05a_virtualstudypops.html | 4 inst/doc/Wambaugh_2018_Figures.html | 4 tests/1comp_test.R | 58 +++ tests/1comp_test.Rout.save | 157 ++++++---- tests/3comp_test.R | 57 +++ tests/3comp_test.Rout.save | 142 ++++++--- tests/3compss_test.R | 50 ++- tests/3compss_test.Rout.save | 67 +++- tests/adddata_test.Rout.save | 14 tests/cheminfo_test.Rout.save | 6 tests/ivive_test.R | 70 ++-- tests/ivive_test.Rout.save | 81 ++--- tests/other_tests.Rout.save | 14 tests/pbtk_test.R | 57 +++ tests/pbtk_test.Rout.save | 133 ++++++-- 40 files changed, 794 insertions(+), 348 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data.
Author: Martin Wilson [cre, aut],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 0.12.0 dated 2018-11-05 and 0.13.0 dated 2019-04-25
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Title: EBGM Disproportionality Scores for Adverse Event Data Mining
Description: An implementation of DuMouchel's (1999)
<doi:10.1080/00031305.1999.10474456> Bayesian data mining method for the
market basket problem. Calculates Empirical Bayes Geometric Mean (EBGM) and
quantile scores from the posterior distribution using the Gamma-Poisson
Shrinker (GPS) model to find unusually large cell counts in large, sparse
contingency tables. Can be used to find unusually high reporting rates of
adverse events associated with products. In general, can be used to mine any
database where the co-occurrence of two variables or items is of interest.
Also calculates relative and proportional reporting ratios. Builds on the work
of the 'PhViD' package, from which much of the code is derived. Some of the
added features include stratification to adjust for confounding variables and
data squashing to improve computational efficiency. Now includes an
implementation of the EM algorithm for hyperparameter estimation loosely
derived from the 'mederrRank' package.
Author: John Ihrie [cre, aut],
Travis Canida [aut],
Ismaïl Ahmed [ctb] (author of 'PhViD' package (derived code)),
Antoine Poncet [ctb] (author of 'PhViD'),
Sergio Venturini [ctb] (author of 'mederrRank' package (derived code)),
Jessica Myers [ctb] (author of 'mederrRank')
Maintainer: John Ihrie <John.Ihrie@fda.hhs.gov>
Diff between openEBGM versions 0.8.1 dated 2019-02-28 and 0.8.2 dated 2019-04-25
DESCRIPTION | 6 +- MD5 | 16 +++---- NEWS | 24 +++-------- R/f_transformInput.R | 6 +- inst/doc/x1_introAndDataPrepVignette.html | 7 ++- inst/doc/x2_rawDataProcessingVignette.html | 7 ++- inst/doc/x3_hyperParameterVignette.html | 53 +++++++++++++------------- inst/doc/x4_posteriorCalculationVignette.html | 13 +++--- inst/doc/x5_openEBGMObjectVignette.html | 7 ++- 9 files changed, 74 insertions(+), 65 deletions(-)
Title: R Front End for 'Apache Spark'
Description: Provides an R Front end for 'Apache Spark' <https://spark.apache.org>.
Author: Shivaram Venkataraman [aut, cre],
Xiangrui Meng [aut],
Felix Cheung [aut],
The Apache Software Foundation [aut, cph]
Maintainer: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Diff between SparkR versions 2.4.1 dated 2019-04-04 and 2.4.2 dated 2019-04-25
DESCRIPTION | 6 ++-- MD5 | 6 ++-- build/vignette.rds |binary inst/doc/sparkr-vignettes.html | 61 +++++++++++++++++++++-------------------- 4 files changed, 38 insertions(+), 35 deletions(-)
Title: Convert Data from and to 'GeoJSON' or 'TopoJSON'
Description: Convert data to 'GeoJSON' or 'TopoJSON' from various R classes,
including vectors, lists, data frames, shape files, and spatial classes.
'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos',
but rather aims to be a high level client to simplify conversions of data
from and to 'GeoJSON' and 'TopoJSON'.
Author: Scott Chamberlain [aut, cre],
Andy Teucher [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between geojsonio versions 0.6.0 dated 2018-03-30 and 0.7.0 dated 2019-04-25
geojsonio-0.6.0/geojsonio/man/geojsonio-deprecated.Rd |only geojsonio-0.6.0/geojsonio/man/lint.Rd |only geojsonio-0.6.0/geojsonio/man/validate.Rd |only geojsonio-0.6.0/geojsonio/tests/testthat/test-lint.R |only geojsonio-0.6.0/geojsonio/tests/testthat/test-validate.R |only geojsonio-0.7.0/geojsonio/DESCRIPTION | 9 geojsonio-0.7.0/geojsonio/LICENSE | 2 geojsonio-0.7.0/geojsonio/MD5 | 98 +++---- geojsonio-0.7.0/geojsonio/NAMESPACE | 31 -- geojsonio-0.7.0/geojsonio/NEWS.md | 19 + geojsonio-0.7.0/geojsonio/R/as.json.R | 4 geojsonio-0.7.0/geojsonio/R/geo_topo.R | 32 +- geojsonio-0.7.0/geojsonio/R/geojson_list.R | 4 geojsonio-0.7.0/geojsonio/R/geojson_sf.R | 4 geojsonio-0.7.0/geojsonio/R/geojson_sp.R | 5 geojsonio-0.7.0/geojsonio/R/geojsonio-package.r | 15 - geojsonio-0.7.0/geojsonio/R/lint.R | 133 ---------- geojsonio-0.7.0/geojsonio/R/topojson_json.R | 12 geojsonio-0.7.0/geojsonio/R/topojson_list.R | 3 geojsonio-0.7.0/geojsonio/R/topojson_read.R | 26 + geojsonio-0.7.0/geojsonio/R/topojson_write.R | 109 ++++---- geojsonio-0.7.0/geojsonio/R/validate.R | 128 --------- geojsonio-0.7.0/geojsonio/README.md | 7 geojsonio-0.7.0/geojsonio/build/vignette.rds |binary geojsonio-0.7.0/geojsonio/inst/doc/geojsonio_vignette.Rmd | 2 geojsonio-0.7.0/geojsonio/inst/doc/geojsonio_vignette.html | 4 geojsonio-0.7.0/geojsonio/inst/img/unnamed-chunk-23-1.png |binary geojsonio-0.7.0/geojsonio/inst/vign/figure/unnamed-chunk-17-1.png |binary geojsonio-0.7.0/geojsonio/inst/vign/geojsonio_vignette.md | 2 geojsonio-0.7.0/geojsonio/man/geo2topo.Rd | 9 geojsonio-0.7.0/geojsonio/man/geojson_json.Rd | 4 geojsonio-0.7.0/geojsonio/man/geojson_list.Rd | 4 geojsonio-0.7.0/geojsonio/man/geojson_sf.Rd | 2 geojsonio-0.7.0/geojsonio/man/geojson_sp.Rd | 5 geojsonio-0.7.0/geojsonio/man/geojson_style.Rd | 8 geojsonio-0.7.0/geojsonio/man/geojsonio-defunct.Rd |only geojsonio-0.7.0/geojsonio/man/geojsonio.Rd | 5 geojsonio-0.7.0/geojsonio/man/lint-defunct.Rd |only geojsonio-0.7.0/geojsonio/man/map_leaf.Rd | 3 geojsonio-0.7.0/geojsonio/man/projections.Rd | 4 geojsonio-0.7.0/geojsonio/man/topojson_json.Rd | 12 geojsonio-0.7.0/geojsonio/man/topojson_list.Rd | 7 geojsonio-0.7.0/geojsonio/man/topojson_read.Rd | 17 - geojsonio-0.7.0/geojsonio/man/topojson_write.Rd | 9 geojsonio-0.7.0/geojsonio/man/validate-defunct.Rd |only geojsonio-0.7.0/geojsonio/tests/testthat/teardown.R |only geojsonio-0.7.0/geojsonio/tests/testthat/test-as.json.R | 8 geojsonio-0.7.0/geojsonio/tests/testthat/test-geo_topo.R | 36 ++ geojsonio-0.7.0/geojsonio/tests/testthat/test-geojson_write.R | 6 geojsonio-0.7.0/geojsonio/tests/testthat/test-map_gist.R | 2 geojsonio-0.7.0/geojsonio/tests/testthat/test-sf_classes.R | 13 geojsonio-0.7.0/geojsonio/tests/testthat/test-topojson_json.R |only geojsonio-0.7.0/geojsonio/tests/testthat/test-topojson_read.R | 42 +-- geojsonio-0.7.0/geojsonio/tests/testthat/test-topojson_write.R | 22 + geojsonio-0.7.0/geojsonio/vignettes/geojsonio_vignette.Rmd | 2 55 files changed, 371 insertions(+), 498 deletions(-)
Title: Extract Genotypes from a PLINK .bed File
Description: A matrix-like data structure that allows for efficient,
convenient, and scalable subsetting of binary genotype/phenotype files
generated by PLINK (<https://www.cog-genomics.org/plink2>), the whole
genome association analysis toolset, without loading the entire file into
memory.
Author: Alexander Grueneberg [aut, cre],
Lian Lian [ctb],
Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between BEDMatrix versions 1.4.1 dated 2018-08-06 and 1.5.0 dated 2019-04-25
DESCRIPTION | 10 +- MD5 | 14 +-- NEWS.md | 9 ++ R/BEDMatrix.R | 75 +++++++++++++---- README.md | 1 man/initialize-BEDMatrix-method.Rd | 9 +- src/BEDMatrix.cpp | 155 +++++++++++++++++++++---------------- tests/testthat/test-BEDMatrix.R | 2 8 files changed, 181 insertions(+), 94 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],
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],
Iain S. Duff [ctb],
John K. Reid [ctb],
Richard Stallman [ctb],
Samuel Thibault [ctb]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.1.2-5 dated 2018-12-18 and 5.1.2-6 dated 2019-04-25
DESCRIPTION | 11 ++++--- MD5 | 31 +++++++++++---------- NAMESPACE | 17 ++++------- NEWS | 11 +++++++ R/RcppExports.R | 14 +++++++++ R/package.R |only R/zzz.R | 4 ++ inst/include/rmumps.h | 13 ++++++++ man/Rmumps.Rd | 2 + man/get_cnst.Rd |only man/rmumps-package.Rd | 2 - src/Makevars | 2 - src/Makevars.seq | 2 - src/RcppExports.cpp | 11 +++++++ src/get_cnst.cpp |only src/rmumps_module.cpp | 63 ++++++++++++++++++++++++++++++++----------- tests/testthat.R | 4 +- tests/testthat/test_rmumps.R | 44 ++++++++++++++++++++++++++++-- 18 files changed, 178 insertions(+), 53 deletions(-)
Title: Public Economic Data and Quantitative Analysis
Description: Provides an interface to access public economic and financial data for
economic research and quantitative analysis. The data sources including
NBS, FRED, Yahoo Finance, 163 Finance and etc.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Diff between pedquant versions 0.1.0 dated 2019-03-15 and 0.1.1 dated 2019-04-25
DESCRIPTION | 12 - MD5 | 40 ++--- NAMESPACE | 6 NEWS.md | 6 R/condition_helper_fun.R | 7 R/ed_nbs.R | 128 +++++++++++------ R/md_2bond.R | 2 R/md_stock1_.R | 7 R/md_stock1_163.R | 169 +++++++++++++--------- R/md_stock_symbol.R | 81 +++-------- R/pq_addti.R | 19 ++ R/pq_backtest.R | 122 +++++++++++++++- R/pq_perf.R | 128 ++++++++++++++++- R/pq_plot.R | 346 ++++++++++++++++++++++++----------------------- R/sysdata.rda |binary man/ed_nbs.Rd | 6 man/ed_nbs_subregion.Rd | 9 - man/ed_nbs_symbol.Rd | 2 man/pq_addti.Rd | 2 man/pq_perf.Rd | 2 man/pq_plot.Rd | 14 - 21 files changed, 710 insertions(+), 398 deletions(-)
Title: Bayesian Model Selection and Averaging for Non-Local and Local
Priors
Description: Bayesian model selection and averaging for regression and mixtures for non-local and selected local priors.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 2.2.1 dated 2019-04-08 and 2.2.2 dated 2019-04-25
ChangeLog | 4 DESCRIPTION | 8 - MD5 | 16 +- R/testfunction.R | 5 inst/doc/mombf.pdf |binary src/cstat.cpp | 128 +++++++++++++++++---- src/cstat.h | 8 + src/modelSel.cpp | 316 +++++++++++++++++++++++++++++++++++++++++------------ src/modelSel.h | 10 + 9 files changed, 386 insertions(+), 109 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>),
Laura J. Graham [ctb] (Input on package structure),
Jeffrey Hollister [ctb] (Input on package structure),
Kimberly A. With [ctb] (Input on package structure),
Florian Privé [ctb] (Original author of underlying C++ code for
get_nearestneighbour() function),
Jeremy VanDerWal [ctb] (Original author of underlying C code for
get_patches() function),
Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between landscapemetrics versions 1.0 dated 2019-03-15 and 1.1 dated 2019-04-25
landscapemetrics-1.0/landscapemetrics/R/get_lsm.R |only landscapemetrics-1.0/landscapemetrics/man/get_lsm.Rd |only landscapemetrics-1.0/landscapemetrics/tests/testthat/test-get-lsm.R |only landscapemetrics-1.1/landscapemetrics/DESCRIPTION | 8 landscapemetrics-1.1/landscapemetrics/MD5 | 414 ++-- landscapemetrics-1.1/landscapemetrics/NAMESPACE | 41 landscapemetrics-1.1/landscapemetrics/NEWS.md | 25 landscapemetrics-1.1/landscapemetrics/R/calculate_lsm.R | 275 +-- landscapemetrics-1.1/landscapemetrics/R/check_landscape.R | 316 +-- landscapemetrics-1.1/landscapemetrics/R/construct_buffer.R | 311 +-- landscapemetrics-1.1/landscapemetrics/R/extract_lsm.R | 763 ++++---- landscapemetrics-1.1/landscapemetrics/R/get_adjacencies.R | 425 +++- landscapemetrics-1.1/landscapemetrics/R/get_boundaries.R | 330 ++- landscapemetrics-1.1/landscapemetrics/R/get_circumscribingcircle.R | 278 ++- landscapemetrics-1.1/landscapemetrics/R/get_nearestneighbour.R | 307 ++- landscapemetrics-1.1/landscapemetrics/R/get_patches.R | 625 +++--- landscapemetrics-1.1/landscapemetrics/R/get_unique_values.R | 468 ++--- landscapemetrics-1.1/landscapemetrics/R/list_lsm.R | 316 ++- landscapemetrics-1.1/landscapemetrics/R/lsm_c_ai.R | 344 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_area_cv.R | 296 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_area_mn.R | 298 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_area_sd.R | 296 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_ca.R | 10 landscapemetrics-1.1/landscapemetrics/R/lsm_c_cai_cv.R | 334 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_cai_mn.R | 328 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_cai_sd.R | 332 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_circle_cv.R | 316 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_circle_mn.R | 310 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_circle_sd.R | 312 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_clumpy.R | 386 ++-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_cohesion.R | 356 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_contig_cv.R | 312 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_contig_mn.R | 312 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_contig_sd.R | 314 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_core_cv.R | 326 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_core_mn.R | 320 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_core_sd.R | 324 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_cpland.R | 354 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_dcad.R | 350 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_dcore_cv.R | 332 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_dcore_mn.R | 326 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_dcore_sd.R | 336 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_division.R | 310 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_ed.R | 356 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_enn_cv.R | 322 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_enn_mn.R | 324 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_enn_sd.R | 324 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_frac_cv.R | 302 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_frac_mn.R | 296 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_frac_sd.R | 300 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_gyrate_cv.R | 310 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_gyrate_mn.R | 308 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_gyrate_sd.R | 308 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_iji.R | 350 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_lpi.R | 300 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_lsi.R | 358 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_mesh.R | 316 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_ndca.R | 330 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_nlsi.R | 386 ++-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_np.R | 306 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_pafrac.R | 392 ++-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_para_cv.R | 296 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_para_mn.R | 296 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_para_sd.R | 296 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_pd.R | 314 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_pladj.R | 298 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_pland.R | 288 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_shape_cv.R | 302 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_shape_mn.R | 302 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_shape_sd.R | 302 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_split.R | 312 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_tca.R | 322 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_c_te.R | 478 ++--- landscapemetrics-1.1/landscapemetrics/R/lsm_l_ai.R | 300 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_area_cv.R | 294 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_area_mn.R | 300 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_area_sd.R | 298 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_cai_cv.R | 362 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_cai_mn.R | 356 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_cai_sd.R | 360 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_circle_cv.R | 308 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_circle_mn.R | 308 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_circle_sd.R | 312 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_cohesion.R | 328 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_condent.R | 353 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_contag.R | 356 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_contig_cv.R | 314 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_contig_mn.R | 312 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_contig_sd.R | 314 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_core_cv.R | 356 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_core_mn.R | 352 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_core_sd.R | 354 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_dcad.R | 374 ++-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_dcore_cv.R | 362 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_dcore_mn.R | 356 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_dcore_sd.R | 360 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_division.R | 306 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_ed.R | 346 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_enn_cv.R | 318 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_enn_mn.R | 318 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_enn_sd.R | 318 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_ent.R | 288 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_frac_cv.R | 302 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_frac_mn.R | 300 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_frac_sd.R | 300 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_gyrate_cv.R | 308 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_gyrate_mn.R | 306 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_gyrate_sd.R | 306 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_iji.R | 354 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_joinent.R | 336 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_lpi.R | 294 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_lsi.R | 354 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_mesh.R | 304 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_msidi.R | 304 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_msiei.R | 294 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_mutinf.R | 350 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_ndca.R | 354 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_np.R | 276 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_pafrac.R | 380 ++-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_para_cv.R | 296 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_para_mn.R | 296 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_para_sd.R | 296 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_pd.R | 320 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_pladj.R | 288 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_pr.R | 252 +- landscapemetrics-1.1/landscapemetrics/R/lsm_l_prd.R | 292 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_rpr.R | 312 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_shape_cv.R | 302 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_shape_mn.R | 302 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_shape_sd.R | 302 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_shdi.R | 280 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_shei.R | 280 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_sidi.R | 288 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_siei.R | 292 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_split.R | 300 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_ta.R | 280 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_tca.R | 350 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_l_te.R | 376 ++-- landscapemetrics-1.1/landscapemetrics/R/lsm_p_area.R | 344 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_p_cai.R | 398 ++-- landscapemetrics-1.1/landscapemetrics/R/lsm_p_circle.R | 444 ++-- landscapemetrics-1.1/landscapemetrics/R/lsm_p_contig.R | 426 ++-- landscapemetrics-1.1/landscapemetrics/R/lsm_p_core.R | 474 ++--- landscapemetrics-1.1/landscapemetrics/R/lsm_p_enn.R | 466 ++--- landscapemetrics-1.1/landscapemetrics/R/lsm_p_frac.R | 336 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_p_gyrate.R | 404 ++-- landscapemetrics-1.1/landscapemetrics/R/lsm_p_ncore.R | 582 +++--- landscapemetrics-1.1/landscapemetrics/R/lsm_p_para.R | 322 +-- landscapemetrics-1.1/landscapemetrics/R/lsm_p_perim.R | 428 ++-- landscapemetrics-1.1/landscapemetrics/R/lsm_p_shape.R | 356 +-- landscapemetrics-1.1/landscapemetrics/R/matrix_to_raster.R | 164 - landscapemetrics-1.1/landscapemetrics/R/pad_raster.R | 507 ++--- landscapemetrics-1.1/landscapemetrics/R/raster_to_points.R | 224 ++ landscapemetrics-1.1/landscapemetrics/R/sample_lsm.R | 676 ++++--- landscapemetrics-1.1/landscapemetrics/R/show_cores.R | 566 +++--- landscapemetrics-1.1/landscapemetrics/R/show_correlation.R | 486 ++--- landscapemetrics-1.1/landscapemetrics/R/show_lsm.R | 613 +++--- landscapemetrics-1.1/landscapemetrics/R/show_patches.R | 446 ++-- landscapemetrics-1.1/landscapemetrics/R/spatialize_lsm.R |only landscapemetrics-1.1/landscapemetrics/R/window_lsm.R | 909 +++++----- landscapemetrics-1.1/landscapemetrics/build/vignette.rds |binary landscapemetrics-1.1/landscapemetrics/inst/doc/getstarted.html | 365 ++-- landscapemetrics-1.1/landscapemetrics/man/calculate_lsm.Rd | 40 landscapemetrics-1.1/landscapemetrics/man/check_landscape.Rd | 14 landscapemetrics-1.1/landscapemetrics/man/construct_buffer.Rd | 39 landscapemetrics-1.1/landscapemetrics/man/extract_lsm.Rd | 97 - landscapemetrics-1.1/landscapemetrics/man/figures/README-unnamed-chunk-1-1.png |binary landscapemetrics-1.1/landscapemetrics/man/get_adjacencies.Rd | 27 landscapemetrics-1.1/landscapemetrics/man/get_boundaries.Rd | 25 landscapemetrics-1.1/landscapemetrics/man/get_circumscribingcircle.Rd | 16 landscapemetrics-1.1/landscapemetrics/man/get_nearestneighbour.Rd | 12 landscapemetrics-1.1/landscapemetrics/man/get_patches.Rd | 5 landscapemetrics-1.1/landscapemetrics/man/get_unique_values.Rd | 3 landscapemetrics-1.1/landscapemetrics/man/list_lsm.Rd | 6 landscapemetrics-1.1/landscapemetrics/man/lsm_l_ent.Rd | 21 landscapemetrics-1.1/landscapemetrics/man/matrix_to_raster.Rd | 2 landscapemetrics-1.1/landscapemetrics/man/pad_raster.Rd | 5 landscapemetrics-1.1/landscapemetrics/man/raster_to_points.Rd | 17 landscapemetrics-1.1/landscapemetrics/man/sample_lsm.Rd | 106 - landscapemetrics-1.1/landscapemetrics/man/show_correlation.Rd | 15 landscapemetrics-1.1/landscapemetrics/man/spatialize_lsm.Rd |only landscapemetrics-1.1/landscapemetrics/man/window_lsm.Rd | 82 landscapemetrics-1.1/landscapemetrics/src/Makevars | 2 landscapemetrics-1.1/landscapemetrics/src/Makevars.win | 2 landscapemetrics-1.1/landscapemetrics/src/RcppExports.cpp | 4 landscapemetrics-1.1/landscapemetrics/src/rcpp_get_coocurrence_matrix.cpp | 3 landscapemetrics-1.1/landscapemetrics/src/rcpp_get_coocurrence_matrix.h | 3 landscapemetrics-1.1/landscapemetrics/src/rcpp_get_coocurrence_matrix_diag.cpp | 2 landscapemetrics-1.1/landscapemetrics/src/rcpp_get_coocurrence_matrix_diag.h | 4 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-calculate-lsm.R | 186 +- landscapemetrics-1.1/landscapemetrics/tests/testthat/test-construct-buffer.R | 48 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-extract-lsm.R | 106 - landscapemetrics-1.1/landscapemetrics/tests/testthat/test-get-adjacencies.R | 103 - landscapemetrics-1.1/landscapemetrics/tests/testthat/test-get-boundaries.R | 87 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-get-circumscribungcircle.R | 131 - landscapemetrics-1.1/landscapemetrics/tests/testthat/test-get-nearestneighbour.R | 51 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-get-unique-values.R | 174 + landscapemetrics-1.1/landscapemetrics/tests/testthat/test-list-lsm.R | 140 + landscapemetrics-1.1/landscapemetrics/tests/testthat/test-lsm-c-ai.R | 58 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-lsm-c-iji.R | 63 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-lsm-c-pafrac.R | 61 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-lsm-l-contag.R | 61 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-lsm-l-iji.R | 63 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-lsm-l-pafrac.R | 61 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-raster-to-points.R | 53 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-sample-lsm.R | 215 +- landscapemetrics-1.1/landscapemetrics/tests/testthat/test-show-cores.R | 100 - landscapemetrics-1.1/landscapemetrics/tests/testthat/test-show-lsm.R | 83 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-show-patches.R | 74 landscapemetrics-1.1/landscapemetrics/tests/testthat/test-spatialize-lsm.R |only landscapemetrics-1.1/landscapemetrics/tests/testthat/test-window-lsm.R | 77 211 files changed, 28769 insertions(+), 26853 deletions(-)
More information about landscapemetrics at CRAN
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Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests
NONMEM output, builds run logs, creates derivative data, generates diagnostics.
NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for
nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between nonmemica versions 0.8.6 dated 2019-02-04 and 0.9.0 dated 2019-04-25
DESCRIPTION | 6 MD5 | 326 ++++++++++++++++++++--------------------- R/bootstrap.R | 4 R/canonical.R | 4 R/definitions.R | 4 R/getset.R | 14 + R/init.R | 48 +++++- R/likebut.R | 33 +++- R/model.R | 39 ++++ R/nonmemica.R | 3 R/partab.R | 8 - R/path.R | 11 + R/superset.R | 25 ++- R/tad.R | 4 R/util.R | 14 + R/xpath.R | 7 inst/doc/parameter-table.html | 68 ++++---- man/as.best.Rd | 19 ++ man/as.bootstrap.Rd | 6 man/as.bootstrap.numeric.Rd | 3 man/as.character.init.Rd | 5 man/as.character.inits.Rd | 5 man/as.character.items.Rd | 5 man/as.character.model.Rd | 5 man/as.init.Rd | 5 man/as.init.numeric.Rd | 3 man/as.inits.Rd | 9 + man/as.inits.numeric.Rd | 3 man/as.matrices.Rd | 4 man/as.matrices.inits.Rd | 4 man/as.matrices.records.Rd | 4 man/as.model.Rd | 9 + man/as.model.numeric.Rd | 5 man/as.omega.Rd | 3 man/as.omega.model.Rd | 3 man/as.tab.Rd | 3 man/as.tab.model.Rd | 3 man/as.theta.Rd | 3 man/as.theta.model.Rd | 3 man/as.xml_document.Rd | 9 + man/as.xml_document.numeric.Rd | 4 man/but.Rd | 3 man/but.default.Rd | 3 man/cash-.init.Rd | 3 man/cash-set-.init.Rd | 3 man/comwidth.Rd | 5 man/comwidth.character.Rd | 4 man/comwidth.inits.Rd | 4 man/comwidth.items.Rd | 4 man/comwidthOne.Rd | 3 man/comwidthOne.character.Rd | 3 man/datafile.Rd | 9 + man/datafile.character.Rd | 9 + man/datafile.numeric.Rd | 9 + man/definitions.Rd | 6 man/definitions.numeric.Rd | 3 man/depends.Rd | 3 man/depends.default.Rd | 3 man/enclose.Rd | 7 man/errors.Rd | 4 man/errors.character.Rd | 3 man/errors.numeric.Rd | 4 man/estimates.Rd | 4 man/estimates.character.Rd | 3 man/estimates.numeric.Rd | 4 man/fixed-set-.init.Rd | 5 man/fixed-set-.inits.Rd | 5 man/fixed-set-.model.Rd | 5 man/fixed-set.Rd | 5 man/fixed.Rd | 13 + man/fixed.model.Rd | 5 man/format.init.Rd | 4 man/format.inits.Rd | 4 man/format.items.Rd | 4 man/format.model.Rd | 4 man/generalize.Rd | 14 + man/grapes-contains-grapes.Rd | 5 man/initDex.Rd | 3 man/initDex.model.Rd | 3 man/initSubscripts.Rd | 3 man/initSubscripts.model.Rd | 3 man/initial-set-.model.Rd | 4 man/initial-set.Rd | 4 man/initial.Rd | 4 man/initial.model.Rd | 4 man/like.Rd | 3 man/like.default.Rd | 3 man/locf.Rd | 25 +++ man/lower-set-.model.Rd | 4 man/lower-set.Rd | 4 man/lower.Rd | 4 man/lower.model.Rd | 4 man/maxWidths.Rd | 3 man/maxWidths.list.Rd | 3 man/meta.Rd | 14 + man/meta.character.Rd | 14 + man/meta.numeric.Rd | 14 + man/metaplot.character.Rd | 13 + man/metaplot.numeric.Rd | 13 + man/metaplot_character.Rd | 13 + man/metasuperset.Rd | 16 +- man/modeldir.Rd | 9 + man/modelfile.Rd | 9 + man/modelpath.Rd | 9 + man/modelpath.character.Rd | 8 + man/modelpath.numeric.Rd | 9 + man/ninput.Rd | 14 + man/ninput.character.Rd | 13 + man/ninput.numeric.Rd | 13 + man/nms_nonmem.Rd | 5 man/nms_nonmem.character.Rd | 5 man/nms_nonmem.model.Rd | 4 man/nms_nonmem.numeric.Rd | 4 man/nonmemica.Rd | 4 man/ord.inits.Rd | 3 man/ord.items.Rd | 3 man/padded.Rd | 7 man/parameters.Rd | 4 man/parameters.character.Rd | 8 - man/parameters.numeric.Rd | 4 man/parens.Rd | 7 man/partab.Rd | 6 man/partab.character.Rd | 3 man/partab.numeric.Rd | 4 man/pool.Rd | 7 man/prettycom.Rd | 3 man/prettycom.character.Rd | 3 man/print.init.Rd | 4 man/print.inits.Rd | 4 man/print.items.Rd | 4 man/print.model.Rd | 4 man/problem.Rd | 4 man/problem.character.Rd | 4 man/problem.numeric.Rd | 4 man/problem_.Rd | 4 man/read.model.Rd | 5 man/runhead.Rd | 7 man/runlog.Rd | 3 man/runlog.character.Rd | 3 man/runlog.numeric.Rd | 4 man/shuffle.Rd | 14 + man/specfile.Rd | 9 + man/specfile.character.Rd | 7 man/specfile.numeric.Rd | 8 + man/sub-.model.Rd | 5 man/sub-sub-.model.Rd | 5 man/superset.Rd | 13 + man/superset.character.Rd | 14 + man/superset.numeric.Rd | 13 + man/superspec.Rd | 13 + man/superspec.character.Rd | 13 + man/superspec.numeric.Rd | 14 + man/tad.Rd | 4 man/text2decimal.Rd | 7 man/tod.Rd | 2 man/updated.Rd | 4 man/updated.character.Rd | 4 man/updated.numeric.Rd | 4 man/upper-set-.model.Rd | 4 man/upper-set.Rd | 4 man/upper.Rd | 4 man/upper.model.Rd | 4 man/write.model.Rd | 5 man/xpath.Rd | 10 + 164 files changed, 1285 insertions(+), 221 deletions(-)
Title: Represent Ordered Lists and Pairs as Strings
Description: Interconverts between ordered lists and compact string notation.
Useful for capturing code lists, and pair-wise codes and decodes, for text storage.
Analogous to factor levels and labels. Generics encode() and decode()
perform interconversion, while codes() and decodes() extract components of an encoding.
The function encoded() checks whether something is interpretable as an encoding.
If a vector has an encoded 'guide' attribute, as_factor() uses it to coerce to factor.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between encode versions 0.3.4 dated 2018-03-28 and 0.3.6 dated 2019-04-25
DESCRIPTION | 9 ++--- MD5 | 32 +++++++++--------- NAMESPACE | 2 + R/encode.R | 83 +++++++++++++++++++++++++++++++++++++++++++++++ man/as_factor.Rd |only man/codes.Rd | 2 + man/codes.default.Rd | 3 + man/decode.Rd | 4 ++ man/decode.data.frame.Rd |only man/decode.default.Rd | 4 ++ man/decodes.Rd | 2 + man/decodes.default.Rd | 3 + man/encode.Rd | 3 + man/encode.character.Rd | 4 ++ man/encode.default.Rd | 4 ++ man/encode.list.Rd | 4 ++ man/encoded.Rd | 2 + man/encoded.default.Rd | 3 + 18 files changed, 145 insertions(+), 19 deletions(-)
Title: Manipulate and Explore UK Biobank Data
Description: A set of tools to create a UK Biobank <http://www.ukbiobank.ac.uk/> dataset from a UKB fileset (.tab, .r, .html),
visualize primary demographic data for a sample subset, query ICD diagnoses,
retrieve genetic metadata, read and write standard file formats for genetic analyses.
Author: Ken Hanscombe [aut, cre]
Maintainer: Ken Hanscombe <ken.hanscombe@gmail.com>
Diff between ukbtools versions 0.11.1 dated 2019-03-14 and 0.11.2 dated 2019-04-25
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NEWS.md | 13 +++++++++++++ R/ukb_dataset.R | 6 +++--- inst/doc/explore-ukb-data.html | 4 ++-- 5 files changed, 29 insertions(+), 16 deletions(-)
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp'
objects. 'OSM' data are extracted from the 'Overpass' web server and
processed with very fast 'C++' routines for return to 'R'.
Author: Mark Padgham [aut, cre],
Bob Rudis [aut],
Robin Lovelace [aut],
Maëlle Salmon [aut],
Andrew Smith [ctb],
James Smith [ctb],
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code),
Finkelstein Noam [ctb, cph] (Author of included stub.R code),
Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmdata versions 0.0.10 dated 2019-03-21 and 0.1.0 dated 2019-04-25
DESCRIPTION | 9 ++++--- MD5 | 44 ++++++++++++++++++++++----------------- NAMESPACE | 1 NEWS.md | 10 ++++++++ R/elevation.R |only R/get-osmdata.R | 16 +++++++------- R/getbb.R | 6 +++-- R/opq.R | 4 +-- R/trim-osmdata.R | 22 ++++++++----------- R/zzz.R | 5 ++++ build/vignette.rds |binary inst/doc/osm-sf-translation.Rmd | 4 +-- inst/doc/osm-sf-translation.html | 8 +++---- inst/doc/osmdata-sc.R |only inst/doc/osmdata-sc.Rmd |only inst/doc/osmdata-sc.html |only inst/doc/osmdata.R | 2 - inst/doc/osmdata.Rmd | 2 - inst/doc/osmdata.html | 6 ++--- man/osm_elevation.Rd |only src/convert-osm-rcpp.cpp | 4 +-- tests/testthat/test-trim.R | 5 ---- tests/testthat/test-unique.R | 18 +++++++++++++++ vignettes/osm-sf-translation.Rmd | 4 +-- vignettes/osmdata-sc.Rmd |only vignettes/osmdata.Rmd | 2 - 26 files changed, 103 insertions(+), 69 deletions(-)
Title: Annotation of Isotopes, Adducts and Fragmentation Adducts for
in-Source LC/MS Metabolomics Data
Description: Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerà and M. Sales-Pardo, Metabolomics Conference (2016), Dublin), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.
Author: Oriol Senan Campos [aut, cre],
Antoni Aguilar-Mogas [aut],
Jordi Capellades [aut],
Miriam Navarro [aut],
Oscar Yanes [aut],
Roger Guimerà [aut],
Marta Sales-Pardo [aut]
Maintainer: Oriol Senan Campos <oriol.senan@urv.cat>
Diff between cliqueMS versions 0.3.0 dated 2019-01-30 and 0.3.1 dated 2019-04-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ build/vignette.rds |binary inst/doc/annotate_features.R | 8 ++++---- inst/doc/annotate_features.Rmd | 8 ++++---- inst/doc/annotate_features.html | 10 +++++----- vignettes/annotate_features.Rmd | 8 ++++---- 8 files changed, 33 insertions(+), 28 deletions(-)
Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use in
photobiology and radiation meteorology and climatology. Calculation of
effective (weighted) and not-weighted irradiances/doses, fluence rates,
transmittance, reflectance, absorptance, absorbance and diverse
ratios and other derived quantities from spectral data. Local maxima and
minima. Conversion between energy- and photon-based units. Wavelength
interpolation. Astronomical calculations related solar angles and day
length. Colours and vision. This package is part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>),
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiology versions 0.9.26 dated 2019-02-12 and 0.9.27 dated 2019-04-25
DESCRIPTION | 18 MD5 | 121 ++-- NEWS | 14 R/meeus.r | 32 - R/mspct.methods.R | 2 R/mspct.row.funs.r | 10 R/on-attach.R | 2 R/photobiology.r | 2 R/rbindspct.r | 4 R/spct.operators.r | 2 R/sun.calc.r | 296 +++++---- R/sun.data.r | 8 R/water.vapour.R | 4 README.md | 20 build/vignette.rds |binary data/A.illuminant.spct.rda |binary data/D2-FEL-constants.rda |binary data/D65.illuminant.spct.rda |binary data/Ler-leaf-spct.rda |binary data/beesxyz.spct.rda |binary data/black_body.spct.rda |binary data/ccd.spct.rda |binary data/ciev10.spct.rda |binary data/ciev2.spct.rda |binary data/ciexyzCC10.spct.rda |binary data/ciexyzCC2.spct.rda |binary data/ciexyzCMF10.spct.rda |binary data/ciexyzCMF2.spct.rda |binary data/clear.spct.rda |binary data/clear_body.spct.rda |binary data/filter-cps-mspct.rda |binary data/green_leaf.spct.rda |binary data/opaque.spct.rda |binary data/photodiode.spct.rda |binary data/polyester.spct.rda |binary data/sun.daily.data.rda |binary data/sun.daily.spct.rda |binary data/sun.data.rda |binary data/sun.spct.rda |binary data/white-led-spct.rda |binary data/white_body.spct.rda |binary data/yellow.gel.rda |binary inst/doc/userguide1-intro.Rmd | 2 inst/doc/userguide1-intro.html | 205 ++++++ inst/doc/userguide2-radiation.html | 1107 ++++++++++++++++++++++--------------- inst/doc/userguide3-astronomy.html | 702 +++++++++++++++-------- man/day_night.Rd | 45 - man/extract.Rd | 2 man/extract_mspct.Rd | 2 man/julian_day.Rd | 16 man/photobiology-package.Rd | 2 man/round.Rd | 2 man/solar_time.Rd | 4 man/sun.daily.data.Rd | 2 man/sun.daily.spct.Rd | 2 man/sun.data.Rd | 2 man/sun.spct.Rd | 2 man/sun_angles.Rd | 42 - man/tz_time_diff.Rd | 2 man/validate_geocode.Rd |only man/water_vp_sat.Rd | 4 vignettes/userguide1-intro.Rmd | 2 62 files changed, 1698 insertions(+), 984 deletions(-)
Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework
<http://taf.ices.dk> to organize data, methods, and results used in ICES
assessments. ICES is an organization facilitating international collaboration
in marine science.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut],
Alexandros Kokkalis [ctb]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between icesTAF versions 2.3-0 dated 2019-04-08 and 3.0-0 dated 2019-04-25
icesTAF-2.3-0/icesTAF/R/utf8.to-latin1.R |only icesTAF-3.0-0/icesTAF/DESCRIPTION | 11 +-- icesTAF-3.0-0/icesTAF/MD5 | 54 +++++++++-------- icesTAF-3.0-0/icesTAF/NAMESPACE | 4 + icesTAF-3.0-0/icesTAF/NEWS | 19 ++++++ icesTAF-3.0-0/icesTAF/R/draft.data.R | 15 ++-- icesTAF-3.0-0/icesTAF/R/draft.software.R | 8 -- icesTAF-3.0-0/icesTAF/R/ds.package.R | 2 icesTAF-3.0-0/icesTAF/R/icesTAF-package.R | 3 icesTAF-3.0-0/icesTAF/R/period.R |only icesTAF-3.0-0/icesTAF/R/process.bib.R | 47 +++++++++++++-- icesTAF-3.0-0/icesTAF/R/taf.bootstrap.R | 5 - icesTAF-3.0-0/icesTAF/R/taf.library.R | 69 +++++++++------------- icesTAF-3.0-0/icesTAF/R/taf.png.R | 15 ++-- icesTAF-3.0-0/icesTAF/R/taf.skeleton.R | 14 +--- icesTAF-3.0-0/icesTAF/R/utf8.to.latin1.R |only icesTAF-3.0-0/icesTAF/R/write.taf.R | 5 + icesTAF-3.0-0/icesTAF/R/zoom.R | 83 ++++++++++++++++++--------- icesTAF-3.0-0/icesTAF/man/draft.data.Rd | 15 ++-- icesTAF-3.0-0/icesTAF/man/draft.software.Rd | 6 - icesTAF-3.0-0/icesTAF/man/icesTAF-package.Rd | 3 icesTAF-3.0-0/icesTAF/man/latin1.to.utf8.Rd | 2 icesTAF-3.0-0/icesTAF/man/period.Rd |only icesTAF-3.0-0/icesTAF/man/process.bib.Rd | 2 icesTAF-3.0-0/icesTAF/man/taf.bootstrap.Rd | 2 icesTAF-3.0-0/icesTAF/man/taf.library.Rd | 46 +++++--------- icesTAF-3.0-0/icesTAF/man/taf.png.Rd | 15 ++-- icesTAF-3.0-0/icesTAF/man/taf.skeleton.Rd | 11 --- icesTAF-3.0-0/icesTAF/man/write.taf.Rd | 3 icesTAF-3.0-0/icesTAF/man/zoom.Rd | 42 +++++++++---- 30 files changed, 297 insertions(+), 204 deletions(-)
Title: Structural Equation and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Author: Timothy C Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>)
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 2.9.9 dated 2019-01-18 and 2.10.0 dated 2019-04-25
umx-2.10.0/umx/DESCRIPTION | 18 umx-2.10.0/umx/INSTALL | 6 umx-2.10.0/umx/MD5 | 475 ++--- umx-2.10.0/umx/NAMESPACE | 37 umx-2.10.0/umx/NEWS.md | 234 +- umx-2.10.0/umx/R/TRHG_code.R |only umx-2.10.0/umx/R/build_run_modify.R |only umx-2.10.0/umx/R/datasets.R | 61 umx-2.10.0/umx/R/deprecated.R | 264 --- umx-2.10.0/umx/R/deprecated_old_twin_versions.R |only umx-2.10.0/umx/R/fit_and_reporting.R |only umx-2.10.0/umx/R/lavanify2ram.R |only umx-2.10.0/umx/R/misc_and_utility.R | 1286 +++++++++------ umx-2.10.0/umx/R/tmx.R | 132 - umx-2.10.0/umx/R/umxACEnew.R | 170 + umx-2.10.0/umx/R/umxIPnew.R |only umx-2.10.0/umx/R/umx_build_high_level_models.R | 6 umx-2.10.0/umx/R/umx_build_polychoricMatrix3.R | 139 + umx-2.10.0/umx/R/umx_build_umxACEcov_fixed.R | 28 umx-2.10.0/umx/R/umx_build_umxACEv.R | 49 umx-2.10.0/umx/R/umx_build_umxGxEbiv.R | 14 umx-2.10.0/umx/R/umx_build_umxSexLim.R | 764 ++++++-- umx-2.10.0/umx/R/umx_build_umxSimplex.R | 22 umx-2.10.0/umx/R/umx_fit_stash_CIs.R | 8 umx-2.10.0/umx/R/umx_fit_umxFitIndices.R | 2 umx-2.10.0/umx/R/xmu.R |only umx-2.10.0/umx/R/xmu_make_top_twin_models.R | 500 ++--- umx-2.10.0/umx/README.md | 25 umx-2.10.0/umx/data/Fischbein_wt.rda |only umx-2.10.0/umx/inst/CITATION | 19 umx-2.10.0/umx/inst/WORDLIST | 26 umx-2.10.0/umx/man/Fischbein_wt.Rd |only umx-2.10.0/umx/man/GFF.Rd | 7 umx-2.10.0/umx/man/RMSEA.MxModel.Rd | 5 umx-2.10.0/umx/man/RMSEA.Rd | 5 umx-2.10.0/umx/man/RMSEA.summary.mxmodel.Rd | 2 umx-2.10.0/umx/man/extractAIC.MxModel.Rd | 2 umx-2.10.0/umx/man/figures/CP.pdf |binary umx-2.10.0/umx/man/figures/CP.png |binary umx-2.10.0/umx/man/figures/IP.pdf |binary umx-2.10.0/umx/man/figures/IP.png |binary umx-2.10.0/umx/man/figures/umx_help_figures.graffle |binary umx-2.10.0/umx/man/install.OpenMx.Rd | 13 umx-2.10.0/umx/man/iqdat.Rd | 3 umx-2.10.0/umx/man/loadings.MxModel.Rd | 11 umx-2.10.0/umx/man/loadings.Rd | 2 umx-2.10.0/umx/man/plot.MxLISRELModel.Rd |only umx-2.10.0/umx/man/plot.MxModel.Rd | 55 umx-2.10.0/umx/man/qm.Rd | 13 umx-2.10.0/umx/man/reliability.Rd | 1 umx-2.10.0/umx/man/residuals.MxModel.Rd | 27 umx-2.10.0/umx/man/tmx_genotypic_effect.Rd | 91 - umx-2.10.0/umx/man/tmx_is.identified.Rd | 9 umx-2.10.0/umx/man/tmx_show.Rd |only umx-2.10.0/umx/man/umx.Rd | 85 umx-2.10.0/umx/man/umxACE.Rd | 185 +- umx-2.10.0/umx/man/umxACE_cov_fixed.Rd | 15 umx-2.10.0/umx/man/umxACEcov.Rd | 26 umx-2.10.0/umx/man/umxACEold.Rd |only umx-2.10.0/umx/man/umxACEv.Rd | 40 umx-2.10.0/umx/man/umxAPA.Rd | 11 umx-2.10.0/umx/man/umxAdd1.Rd | 2 umx-2.10.0/umx/man/umxAlgebra.Rd | 12 umx-2.10.0/umx/man/umxBrownie.Rd | 13 umx-2.10.0/umx/man/umxCI.Rd | 2 umx-2.10.0/umx/man/umxCI_boot.Rd | 26 umx-2.10.0/umx/man/umxCP.Rd | 77 umx-2.10.0/umx/man/umxCPold.Rd | 14 umx-2.10.0/umx/man/umxCompare.Rd | 2 umx-2.10.0/umx/man/umxConfint.Rd | 2 umx-2.10.0/umx/man/umxCov2cor.Rd | 14 umx-2.10.0/umx/man/umxCovData.Rd | 3 umx-2.10.0/umx/man/umxDescribeDataWLS.Rd |only umx-2.10.0/umx/man/umxDiagnose.Rd | 26 umx-2.10.0/umx/man/umxDrop1.Rd | 2 umx-2.10.0/umx/man/umxEFA.Rd | 3 umx-2.10.0/umx/man/umxEquate.Rd | 6 umx-2.10.0/umx/man/umxEval.Rd | 9 umx-2.10.0/umx/man/umxExamples.Rd |only umx-2.10.0/umx/man/umxExpCov.Rd | 18 umx-2.10.0/umx/man/umxExpMeans.Rd | 18 umx-2.10.0/umx/man/umxFactor.Rd | 13 umx-2.10.0/umx/man/umxFactorScores.Rd | 13 umx-2.10.0/umx/man/umxFixAll.Rd | 2 umx-2.10.0/umx/man/umxGetParameters.Rd | 15 umx-2.10.0/umx/man/umxGxE.Rd | 13 umx-2.10.0/umx/man/umxGxE_window.Rd | 6 umx-2.10.0/umx/man/umxGxEbiv.Rd | 11 umx-2.10.0/umx/man/umxHetCor.Rd | 1 umx-2.10.0/umx/man/umxIP.Rd | 166 + umx-2.10.0/umx/man/umxIPold.Rd |only umx-2.10.0/umx/man/umxJiggle.Rd | 2 umx-2.10.0/umx/man/umxLabel.Rd | 12 umx-2.10.0/umx/man/umxLatent.Rd | 4 umx-2.10.0/umx/man/umxLav2RAM.Rd |only umx-2.10.0/umx/man/umxMI.Rd | 2 umx-2.10.0/umx/man/umxMatrix.Rd | 43 umx-2.10.0/umx/man/umxModel.Rd | 10 umx-2.10.0/umx/man/umxModify.Rd | 16 umx-2.10.0/umx/man/umxPadAndPruneForDefVars.Rd | 1 umx-2.10.0/umx/man/umxPath.Rd | 12 umx-2.10.0/umx/man/umxPlotACE.Rd | 15 umx-2.10.0/umx/man/umxPlotACEcov.Rd | 15 umx-2.10.0/umx/man/umxPlotACEv.Rd | 13 umx-2.10.0/umx/man/umxPlotCP.Rd | 36 umx-2.10.0/umx/man/umxPlotCPold.Rd |only umx-2.10.0/umx/man/umxPlotGxE.Rd | 15 umx-2.10.0/umx/man/umxPlotGxEbiv.Rd | 13 umx-2.10.0/umx/man/umxPlotIP.Rd | 17 umx-2.10.0/umx/man/umxPlotSexLim.Rd |only umx-2.10.0/umx/man/umxPlotSimplex.Rd | 11 umx-2.10.0/umx/man/umxRAM.Rd | 170 + umx-2.10.0/umx/man/umxRAM2.Rd |only umx-2.10.0/umx/man/umxRAM2Ordinal.Rd | 19 umx-2.10.0/umx/man/umxReduce.Rd | 22 umx-2.10.0/umx/man/umxReduceACE.Rd | 5 umx-2.10.0/umx/man/umxReduceGxE.Rd | 5 umx-2.10.0/umx/man/umxRun.Rd | 23 umx-2.10.0/umx/man/umxSetParameters.Rd | 2 umx-2.10.0/umx/man/umxSexLim.Rd | 204 +- umx-2.10.0/umx/man/umxSimplex.Rd | 8 umx-2.10.0/umx/man/umxSummarizeTwinData.Rd | 7 umx-2.10.0/umx/man/umxSummary.MxModel.Rd | 2 umx-2.10.0/umx/man/umxSummary.Rd | 19 umx-2.10.0/umx/man/umxSummaryACE.Rd | 6 umx-2.10.0/umx/man/umxSummaryACEcov.Rd | 6 umx-2.10.0/umx/man/umxSummaryACEv.Rd | 4 umx-2.10.0/umx/man/umxSummaryCP.Rd | 6 umx-2.10.0/umx/man/umxSummaryGxE.Rd | 6 umx-2.10.0/umx/man/umxSummaryGxEbiv.Rd | 4 umx-2.10.0/umx/man/umxSummaryIP.Rd | 6 umx-2.10.0/umx/man/umxSummarySexLim.Rd | 61 umx-2.10.0/umx/man/umxSummarySimplex.Rd | 4 umx-2.10.0/umx/man/umxSuperModel.Rd | 16 umx-2.10.0/umx/man/umxThresholdMatrix.Rd | 10 umx-2.10.0/umx/man/umxTwoStage.Rd | 1 umx-2.10.0/umx/man/umxUnexplainedCausalNexus.Rd | 2 umx-2.10.0/umx/man/umxValues.Rd | 9 umx-2.10.0/umx/man/umxVersion.Rd | 13 umx-2.10.0/umx/man/umxWeightedAIC.Rd | 18 umx-2.10.0/umx/man/umx_APA_pval.Rd | 16 umx-2.10.0/umx/man/umx_aggregate.Rd | 12 umx-2.10.0/umx/man/umx_array_shift.Rd | 13 umx-2.10.0/umx/man/umx_as_numeric.Rd | 1 umx-2.10.0/umx/man/umx_cell_is_on.Rd | 21 umx-2.10.0/umx/man/umx_check_model.Rd | 15 umx-2.10.0/umx/man/umx_cont_2_quantiles.Rd | 13 umx-2.10.0/umx/man/umx_cov2raw.Rd | 1 umx-2.10.0/umx/man/umx_default_option.Rd | 1 umx-2.10.0/umx/man/umx_dot_define_shapes.Rd |only umx-2.10.0/umx/man/umx_dot_mat2dot.Rd |only umx-2.10.0/umx/man/umx_dot_rank.Rd |only umx-2.10.0/umx/man/umx_find_object.Rd | 5 umx-2.10.0/umx/man/umx_fix_first_loadings.Rd | 38 umx-2.10.0/umx/man/umx_fix_latents.Rd | 20 umx-2.10.0/umx/man/umx_fun_mean_sd.Rd | 2 umx-2.10.0/umx/man/umx_get_bracket_addresses.Rd | 17 umx-2.10.0/umx/man/umx_get_checkpoint.Rd | 1 umx-2.10.0/umx/man/umx_get_options.Rd | 1 umx-2.10.0/umx/man/umx_has_CIs.Rd | 16 umx-2.10.0/umx/man/umx_has_been_run.Rd | 14 umx-2.10.0/umx/man/umx_has_means.Rd | 15 umx-2.10.0/umx/man/umx_is_RAM.Rd | 17 umx-2.10.0/umx/man/umx_is_cov.Rd | 2 umx-2.10.0/umx/man/umx_lower2full.Rd | 1 umx-2.10.0/umx/man/umx_make.Rd | 16 umx-2.10.0/umx/man/umx_make_MR_data.Rd | 1 umx-2.10.0/umx/man/umx_make_TwinData.Rd | 1 umx-2.10.0/umx/man/umx_make_bin_cont_pair_data.Rd | 1 umx-2.10.0/umx/man/umx_make_fake_data.Rd | 1 umx-2.10.0/umx/man/umx_make_sql_from_excel.Rd | 10 umx-2.10.0/umx/man/umx_merge_CIs.Rd | 1 umx-2.10.0/umx/man/umx_msg.Rd | 6 umx-2.10.0/umx/man/umx_names.Rd | 19 umx-2.10.0/umx/man/umx_open_CRAN_page.Rd | 11 umx-2.10.0/umx/man/umx_pad.Rd | 8 umx-2.10.0/umx/man/umx_parameters.Rd | 12 umx-2.10.0/umx/man/umx_pb_note.Rd | 11 umx-2.10.0/umx/man/umx_polychoric.Rd | 17 umx-2.10.0/umx/man/umx_polypairwise.Rd | 16 umx-2.10.0/umx/man/umx_polytriowise.Rd | 15 umx-2.10.0/umx/man/umx_print.Rd | 21 umx-2.10.0/umx/man/umx_r_test.Rd | 2 umx-2.10.0/umx/man/umx_read_lower.Rd | 30 umx-2.10.0/umx/man/umx_rename.Rd | 5 umx-2.10.0/umx/man/umx_reorder.Rd | 1 umx-2.10.0/umx/man/umx_scale.Rd | 11 umx-2.10.0/umx/man/umx_score_scale.Rd | 43 umx-2.10.0/umx/man/umx_set_auto_plot.Rd | 1 umx-2.10.0/umx/man/umx_set_auto_run.Rd | 1 umx-2.10.0/umx/man/umx_set_checkpoint.Rd | 1 umx-2.10.0/umx/man/umx_set_condensed_slots.Rd | 1 umx-2.10.0/umx/man/umx_set_cores.Rd | 1 umx-2.10.0/umx/man/umx_set_data_variance_check.Rd |only umx-2.10.0/umx/man/umx_set_optimization_options.Rd | 1 umx-2.10.0/umx/man/umx_set_optimizer.Rd | 1 umx-2.10.0/umx/man/umx_set_plot_file_suffix.Rd | 1 umx-2.10.0/umx/man/umx_set_plot_format.Rd | 1 umx-2.10.0/umx/man/umx_set_table_format.Rd | 1 umx-2.10.0/umx/man/umx_show_fit_or_comparison.Rd | 10 umx-2.10.0/umx/man/umx_stack.Rd | 1 umx-2.10.0/umx/man/umx_standardize_ACE.Rd | 1 umx-2.10.0/umx/man/umx_standardize_ACEcov.Rd | 1 umx-2.10.0/umx/man/umx_standardize_ACEv.Rd | 1 umx-2.10.0/umx/man/umx_standardize_CP.Rd | 1 umx-2.10.0/umx/man/umx_standardize_IP.Rd | 1 umx-2.10.0/umx/man/umx_standardize_RAM.Rd | 23 umx-2.10.0/umx/man/umx_standardize_SexLim.Rd |only umx-2.10.0/umx/man/umx_standardize_Simplex.Rd | 1 umx-2.10.0/umx/man/umx_stash_CIs.Rd | 7 umx-2.10.0/umx/man/umx_string_to_algebra.Rd | 2 umx-2.10.0/umx/man/umx_swap_a_block.Rd | 1 umx-2.10.0/umx/man/umx_time.Rd | 8 umx-2.10.0/umx/man/umx_trim.Rd | 13 umx-2.10.0/umx/man/us_skinfold_data.Rd | 9 umx-2.10.0/umx/man/xmuHasSquareBrackets.Rd | 10 umx-2.10.0/umx/man/xmuLabel_MATRIX_Model.Rd | 10 umx-2.10.0/umx/man/xmuLabel_Matrix.Rd | 10 umx-2.10.0/umx/man/xmuLabel_RAM_Model.Rd | 22 umx-2.10.0/umx/man/xmuMI.Rd | 10 umx-2.10.0/umx/man/xmuMakeDeviationThresholdsMatrices.Rd | 10 umx-2.10.0/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 10 umx-2.10.0/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 10 umx-2.10.0/umx/man/xmuMaxLevels.Rd | 10 umx-2.10.0/umx/man/xmuMinLevels.Rd | 10 umx-2.10.0/umx/man/xmuPropagateLabels.Rd | 10 umx-2.10.0/umx/man/xmu_assemble_twin_supermodel.Rd | 14 umx-2.10.0/umx/man/xmu_check_levels_identical.Rd | 10 umx-2.10.0/umx/man/xmu_check_variance.Rd |only umx-2.10.0/umx/man/xmu_clean_label.Rd |only umx-2.10.0/umx/man/xmu_dot_make_paths.Rd | 17 umx-2.10.0/umx/man/xmu_dot_make_residuals.Rd | 17 umx-2.10.0/umx/man/xmu_dot_maker.Rd | 39 umx-2.10.0/umx/man/xmu_dot_move_ranks.Rd |only umx-2.10.0/umx/man/xmu_dot_rank_str.Rd |only umx-2.10.0/umx/man/xmu_get_CI.Rd |only umx-2.10.0/umx/man/xmu_lavaan_process_group.Rd |only umx-2.10.0/umx/man/xmu_make_mxData.Rd | 46 umx-2.10.0/umx/man/xmu_make_top_twin.Rd |only umx-2.10.0/umx/man/xmu_model_needs_means.Rd |only umx-2.10.0/umx/man/xmu_safe_run_summary.Rd | 14 umx-2.10.0/umx/man/xmu_set_sep_from_suffix.Rd | 10 umx-2.10.0/umx/man/xmu_simplex_corner.Rd | 10 umx-2.10.0/umx/man/xmu_start_value_list.Rd | 10 umx-2.10.0/umx/man/xmu_starts.Rd | 12 umx-2.10.0/umx/man/xmu_twin_check.Rd | 7 umx-2.10.0/umx/tests/testthat/test_umx_rename.r | 2 umx-2.10.0/umx/tests/testthat/test_xmu_make_mxData.r |only umx-2.9.9/umx/R/build_run_modify.r |only umx-2.9.9/umx/R/fit_and_reporting.r |only umx-2.9.9/umx/R/umx_fit_umxPlotCPnew.R |only umx-2.9.9/umx/R/xmu.r |only umx-2.9.9/umx/R/xmu_mean_var_starts.R |only umx-2.9.9/umx/man/umxACEnew.Rd |only umx-2.9.9/umx/man/umxIPnew.Rd |only umx-2.9.9/umx/man/umxPlotCPnew.Rd |only umx-2.9.9/umx/man/umx_APA_model_CI.Rd |only umx-2.9.9/umx/man/umx_add_variances.Rd |only umx-2.9.9/umx/man/umx_graphviz_rank.Rd |only umx-2.9.9/umx/man/umx_mat2dot.Rd |only umx-2.9.9/umx/man/umx_show.Rd |only umx-2.9.9/umx/man/xmu_make_top_twin_models.Rd |only 262 files changed, 4278 insertions(+), 2920 deletions(-)
Title: Excerpt Structuring Comments from Your Code File and Set a Table
of Contents
Description: This is an R interface to the
python package 'excerpts' (<https://pypi.python.org/pypi/excerpts>).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between excerptr versions 1.4.1 dated 2018-06-03 and 2.0.0 dated 2019-04-25
excerptr-1.4.1/excerptr/R/get_excerpts.R |only excerptr-1.4.1/excerptr/R/internals.R |only excerptr-1.4.1/excerptr/R/options.R |only excerptr-1.4.1/excerptr/R/utils.R |only excerptr-1.4.1/excerptr/inst/doc/excerptr_Introduction.R |only excerptr-1.4.1/excerptr/inst/doc/excerptr_Introduction.Rmd |only excerptr-1.4.1/excerptr/inst/doc/excerptr_Introduction.html |only excerptr-1.4.1/excerptr/inst/tests/testthat |only excerptr-1.4.1/excerptr/inst/tests/testthat.R |only excerptr-1.4.1/excerptr/man/concatenate_python_codes.Rd |only excerptr-1.4.1/excerptr/man/construct_path.Rd |only excerptr-1.4.1/excerptr/man/get_excerpts.Rd |only excerptr-1.4.1/excerptr/man/get_excerpts_path.Rd |only excerptr-1.4.1/excerptr/man/load_excerpts.Rd |only excerptr-1.4.1/excerptr/man/set_excertps_path.Rd |only excerptr-1.4.1/excerptr/tests/files |only excerptr-1.4.1/excerptr/tests/testthat/test_basic.R |only excerptr-1.4.1/excerptr/vignettes/excerptr_Introduction.Rmd |only excerptr-2.0.0/excerptr/DESCRIPTION | 26 +- excerptr-2.0.0/excerptr/MD5 | 54 ++---- excerptr-2.0.0/excerptr/NAMESPACE | 2 excerptr-2.0.0/excerptr/NEWS.md | 8 excerptr-2.0.0/excerptr/R/excerptr-package.R | 4 excerptr-2.0.0/excerptr/R/excerptr.R | 88 +++------- excerptr-2.0.0/excerptr/R/throw.R |only excerptr-2.0.0/excerptr/R/zzz.R | 10 - excerptr-2.0.0/excerptr/README.md | 78 ++------ excerptr-2.0.0/excerptr/build/vignette.rds |binary excerptr-2.0.0/excerptr/inst/doc/An_Introduction_to_excerptr.R |only excerptr-2.0.0/excerptr/inst/doc/An_Introduction_to_excerptr.Rmd |only excerptr-2.0.0/excerptr/inst/doc/An_Introduction_to_excerptr.html |only excerptr-2.0.0/excerptr/inst/runit_tests |only excerptr-2.0.0/excerptr/inst/tests/files/some_file.tex |only excerptr-2.0.0/excerptr/inst/tests/runit.R |only excerptr-2.0.0/excerptr/man/excerptr-package.Rd | 5 excerptr-2.0.0/excerptr/man/excerptr.Rd | 20 +- excerptr-2.0.0/excerptr/man/throw.Rd |only excerptr-2.0.0/excerptr/tests/runit.R |only excerptr-2.0.0/excerptr/tests/testthat.R | 5 excerptr-2.0.0/excerptr/tests/testthat/test-basic.R |only excerptr-2.0.0/excerptr/tests/testthat/test-throw.R |only excerptr-2.0.0/excerptr/vignettes/An_Introduction_to_excerptr.Rmd |only 42 files changed, 108 insertions(+), 192 deletions(-)
Title: Easily Encrypt and Decrypt Data Frame/Tibble Columns or Files
using RSA Public/Private Keys
Description: It is important to ensure that sensitive data is protected.
This straightforward package is aimed at the end-user.
Strong RSA encryption using a public/private key pair is used to encrypt data frame or tibble columns.
A public key can be shared to allow others to encrypt data to be sent to you.
This is particularly aimed a healthcare settings so patient data can be pseudonymised.
Author: Cameron Fairfield [aut],
Riinu Ots [aut],
Stephen Knight [aut],
Tom Drake [aut],
Ewen Harrison [aut, cre]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between encryptr versions 0.1.2 dated 2019-03-25 and 0.1.3 dated 2019-04-25
encryptr-0.1.2/encryptr/R/finalencrypt-internal_functions.R |only encryptr-0.1.3/encryptr/DESCRIPTION | 10 - encryptr-0.1.3/encryptr/MD5 | 37 +++--- encryptr-0.1.3/encryptr/NAMESPACE | 2 encryptr-0.1.3/encryptr/NEWS.md | 5 encryptr-0.1.3/encryptr/R/decrypt.R | 28 +++- encryptr-0.1.3/encryptr/R/decrypt_file.R |only encryptr-0.1.3/encryptr/R/encrypt.R | 22 ++- encryptr-0.1.3/encryptr/R/encrypt_file.R |only encryptr-0.1.3/encryptr/R/encryptr-internal_functions.R |only encryptr-0.1.3/encryptr/R/genkeys.R | 13 ++ encryptr-0.1.3/encryptr/README.md | 59 ++++++++-- encryptr-0.1.3/encryptr/man/assign_to_global.Rd | 2 encryptr-0.1.3/encryptr/man/decrypt.Rd | 26 +++- encryptr-0.1.3/encryptr/man/decrypt_file.Rd |only encryptr-0.1.3/encryptr/man/encrypt.Rd | 20 ++- encryptr-0.1.3/encryptr/man/encrypt_file.Rd |only encryptr-0.1.3/encryptr/man/genkeys.Rd | 3 encryptr-0.1.3/encryptr/man/hex2raw.Rd | 2 encryptr-0.1.3/encryptr/man/pipe.Rd | 2 encryptr-0.1.3/encryptr/man/raw2hex.Rd | 2 encryptr-0.1.3/encryptr/tests/testthat/tests-encrypt_decrypt.R |only encryptr-0.1.3/encryptr/tests/testthat/tests-genkeys.R | 5 23 files changed, 176 insertions(+), 62 deletions(-)
Title: Power Calculations for Assessing Correlates of Risk in Clinical
Efficacy Trials
Description: Calculates power for assessment of intermediate biomarker responses as correlates of risk in the active treatment group in clinical efficacy trials, as described in Gilbert, Janes, and Huang, Power/Sample Size Calculations for Assessing Correlates of Risk in Clinical Efficacy Trials (2016, Statistics in Medicine). The methods differ from past approaches by accounting for the level of clinical treatment efficacy overall and in biomarker response subgroups, which enables the correlates of risk results to be interpreted in terms of potential correlates of efficacy/protection. The methods also account for inter-individual variability of the observed biomarker response that is not biologically relevant (e.g., due to technical measurement error of the laboratory assay used to measure the biomarker response), which is important because power to detect a specified correlate of risk effect size is heavily affected by the biomarker's measurement error. The methods can be used for a general binary clinical endpoint model with a univariate dichotomous, trichotomous, or continuous biomarker response measured in active treatment recipients at a fixed timepoint after randomization, with either case-cohort Bernoulli sampling or case-control without-replacement sampling of the biomarker (a baseline biomarker is handled as a trivial special case). In a specified two-group trial design, the computeN() function can initially be used for calculating additional requisite design parameters pertaining to the target population of active treatment recipients observed to be at risk at the biomarker sampling timepoint. Subsequently, the power calculation employs an inverse probability weighted logistic regression model fitted by the tps() function in the 'osDesign' package. Power results as well as the relationship between the correlate of risk effect size and treatment efficacy can be visualized using various plotting functions. To link power calculations for detecting a correlate of risk and a correlate of treatment efficacy, a baseline immunogenicity predictor (BIP) can be simulated according to a specified classification rule (for dichotomous or trichotomous BIPs) or correlation with the biomarker response (for continuous BIPs), then outputted along with biomarker response data under assignment to treatment, and clinical endpoint data for both treatment and placebo groups.
Author: Stephanie Wu [aut],
Michal Juraska [aut, cre],
Peter Gilbert [aut],
Yunda Huang [aut]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between CoRpower versions 1.0.0 dated 2018-10-06 and 1.0.1 dated 2019-04-25
CoRpower-1.0.0/CoRpower/inst/doc/CoRpower.R |only CoRpower-1.0.0/CoRpower/inst/doc/CoRpower.Rmd |only CoRpower-1.0.0/CoRpower/inst/doc/CoRpower.html |only CoRpower-1.0.0/CoRpower/vignettes/CoRpower.Rmd |only CoRpower-1.0.1/CoRpower/DESCRIPTION | 18 CoRpower-1.0.1/CoRpower/MD5 | 37 CoRpower-1.0.1/CoRpower/R/computeN.R | 14 CoRpower-1.0.1/CoRpower/R/computePower.R | 1551 ++++++---- CoRpower-1.0.1/CoRpower/R/plotPowerCont.R | 42 CoRpower-1.0.1/CoRpower/R/plotPowerTri.R | 94 CoRpower-1.0.1/CoRpower/R/plotRRgradVE.R | 39 CoRpower-1.0.1/CoRpower/R/plotVElatCont.R | 35 CoRpower-1.0.1/CoRpower/build/vignette.rds |binary CoRpower-1.0.1/CoRpower/inst/doc/CoRpowerIntroduction.R |only CoRpower-1.0.1/CoRpower/inst/doc/CoRpowerIntroduction.Rmd |only CoRpower-1.0.1/CoRpower/inst/doc/CoRpowerIntroduction.html |only CoRpower-1.0.1/CoRpower/inst/doc/placeboAndBIPdataSimulationAlgorithms.Rmd |only CoRpower-1.0.1/CoRpower/inst/doc/placeboAndBIPdataSimulationAlgorithms.html |only CoRpower-1.0.1/CoRpower/man/computePower.Rd | 264 + CoRpower-1.0.1/CoRpower/man/plotPowerCont.Rd | 25 CoRpower-1.0.1/CoRpower/man/plotPowerTri.Rd | 27 CoRpower-1.0.1/CoRpower/man/plotRRgradVE.Rd | 17 CoRpower-1.0.1/CoRpower/man/plotVElatCont.Rd | 22 CoRpower-1.0.1/CoRpower/vignettes/CoRpowerIntroduction.Rmd |only CoRpower-1.0.1/CoRpower/vignettes/placeboAndBIPdataSimulationAlgorithms.Rmd |only 25 files changed, 1387 insertions(+), 798 deletions(-)
Title: R Interface for China National Data
Description: R interface for china national data <http://data.stats.gov.cn/>,
some convenient functions for accessing the national data are provided.
Author: Xuehui YANG
Maintainer: Xuehui YANG <jianghang@bagualu.net>
Diff between rstatscn versions 1.1.1 dated 2016-07-20 and 1.1.3 dated 2019-04-25
DESCRIPTION | 15 - MD5 | 30 +- NAMESPACE | 21 - NEWS.md | 52 ++-- R/rstatscn.R | 531 ++++++++++++++++++++++---------------------- README.md | 24 - man/checkHttpStatus.Rd | 35 +- man/dataJson2df.Rd | 43 +-- man/genDfwds.Rd | 45 +-- man/milSec.Rd | 29 +- man/statscnDbs.Rd | 35 +- man/statscnQueryData.Rd | 73 +++--- man/statscnQueryLastN.Rd | 47 +-- man/statscnQueryZb.Rd | 51 ++-- man/statscnRegions.Rd | 47 +-- man/statscnRowNamePrefix.Rd | 51 ++-- 16 files changed, 576 insertions(+), 553 deletions(-)
Title: A Data Specification Format and Interface
Description: Creates a data specification that describes the columns of a
table (data.frame). Provides methods to read, write, and update the
specification. Checks whether a table matches its specification. See
specification.data.frame(),read.spec(), write.spec(), as.csv.spec(),
respecify.character(), and %matches%.data.frame().
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between spec versions 0.1.6 dated 2019-02-04 and 0.1.7 dated 2019-04-25
DESCRIPTION | 6 ++-- MD5 | 46 +++++++++++++++---------------- R/spec.R | 40 ++++++++++++++++++++++++++ man/as.spec.Rd | 5 +++ man/as.spec.character.Rd | 5 +++ man/as.spec.data.frame.Rd | 5 +++ man/grapes-matches-grapes-.character.Rd | 4 ++ man/grapes-matches-grapes-.data.frame.Rd | 4 ++ man/grapes-matches-grapes-.spec.Rd | 5 +++ man/grapes-matches-grapes.Rd | 5 +++ man/guidetext.Rd | 2 - man/guidetext.spec.Rd | 3 ++ man/read.spec.Rd | 5 +++ man/respecify.Rd | 4 ++ man/respecify.character.Rd | 4 ++ man/respecify.spec.Rd | 4 ++ man/specification.Rd | 5 +++ man/specification.comment.Rd | 5 +++ man/specification.data.frame.Rd | 4 ++ man/specification.default.Rd | 5 +++ man/specify.Rd | 4 ++ man/specify.character.Rd | 4 ++ man/specify.data.frame.Rd | 4 ++ man/write.spec.Rd | 5 +++ 24 files changed, 155 insertions(+), 28 deletions(-)
Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows
for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rqdatatable versions 1.1.4 dated 2019-02-25 and 1.1.5 dated 2019-04-25
DESCRIPTION | 12 ++++++------ MD5 | 17 +++++++++++------ NAMESPACE | 3 +++ NEWS.md | 4 ++++ R/data_table_exports.R |only README.md | 4 ++++ inst/doc/GroupedSampling.html | 9 ++++++--- inst/doc/logisticexample.html | 9 ++++++--- inst/unit_tests/test_dt_exports.R |only man/layout_to_blocks_data_table.Rd |only man/layout_to_rowrecs_data_table.Rd |only man/rbindlist_data_table.Rd |only 12 files changed, 40 insertions(+), 18 deletions(-)
Title: Optimally Robust Estimation
Description: Optimally robust estimation in general smoothly parameterized models using S4
classes and methods.
Author: Matthias Kohl [cre, cph],
Mykhailo Pupashenko [ctb] (contributed wrapper functions for diagnostic
plots),
Gerald Kroisandt [ctb] (contributed testing routines),
Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between ROptEst versions 1.2.0 dated 2019-04-07 and 1.2.1 dated 2019-04-25
DESCRIPTION | 16 ++-- MD5 | 8 +- R/CheckMakeContIC.R | 32 ++++++--- inst/NEWS | 12 +++ man/0ROptEst-package.Rd | 159 +++++++++++++++++++++++------------------------- 5 files changed, 124 insertions(+), 103 deletions(-)
Title: Robust Asymptotic Statistics
Description: Base S4-classes and functions for robust asymptotic statistics.
Author: Matthias Kohl [cre, cph, aut],
Peter Ruckdeschel [aut, cph],
Mykhailo Pupashenko [ctb] (contributed wrapper functions for diagnostic
plots),
Gerald Kroisandt [ctb] (contributed testing routines),
R Core Team [ctb, cph] (for source file 'format.perc')
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between RobAStBase versions 1.2.0 dated 2019-04-05 and 1.2.1 dated 2019-04-25
DESCRIPTION | 16 MD5 | 14 R/CheckMakeIC.R | 36 +- R/plotWrapper.R | 305 ++---------------- inst/NEWS | 35 +- man/0RobAStBase-package.Rd | 111 +++--- man/comparePlot.Rd | 740 ++++++++++++++++++++++---------------------- man/internal_GridHelpers.Rd | 128 +++---- 8 files changed, 587 insertions(+), 798 deletions(-)
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F.Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between mvSLOUCH versions 2.0.4 dated 2019-04-11 and 2.0.5 dated 2019-04-25
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/regimes.R | 10 +++++++++- man/estimate.evolutionary.model.Rd | 5 ++++- man/mvslouchModel.Rd | 7 +++++-- man/ouchModel.Rd | 5 ++++- man/parametric.bootstrap.Rd | 5 ++++- 7 files changed, 36 insertions(+), 16 deletions(-)
Title: Interval and Enum-Type Representation of Vectors
Description: Enum-type representation of vectors and representation
of intervals, including a method of coercing variables in data frames.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between inum versions 1.0-0 dated 2017-12-12 and 1.0-1 dated 2019-04-25
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- R/inum.R | 6 +++++- inst/NEWS.Rd | 7 +++++++ tests/bugfixes.R |only tests/bugfixes.Rout.save |only tests/regtest.R | 1 + tests/regtest.Rout.save | 7 ++++--- 8 files changed, 28 insertions(+), 13 deletions(-)
Title: Parse Darwin Core Files
Description: Parse and create Darwin Core (<http://rs.tdwg.org/dwc/>) Simple
and Archives. Functionality includes reading and parsing all the
files in a Darwin Core Archive, including the datasets and metadata;
read and parse simple Darwin Core files; and validation of Darwin
Core Archives.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between finch versions 0.2.0 dated 2018-01-25 and 0.3.0 dated 2019-04-25
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/dwca.R | 4 ++-- README.md | 1 + tests/testthat/test-dwca_get.R | 8 ++++---- 6 files changed, 27 insertions(+), 17 deletions(-)
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Developed at Cito, The Netherlands, with subsidy from the Dutch Ministry of Education, Culture, and Science.
Author: Gunter Maris, Timo Bechger, Jesse Koops, Ivailo Partchev
Maintainer: Ivailo Partchev <partchev@gmail.com>
Diff between dexter versions 0.8.4 dated 2019-01-02 and 0.8.5 dated 2019-04-25
dexter-0.8.4/dexter/man/design_is_connected.Rd |only dexter-0.8.5/dexter/DESCRIPTION | 6 dexter-0.8.5/dexter/MD5 | 48 +- dexter-0.8.5/dexter/NAMESPACE | 3 dexter-0.8.5/dexter/NEWS | 8 dexter-0.8.5/dexter/R/anon_calibration.R | 30 - dexter-0.8.5/dexter/R/anon_plausible_values.R | 2 dexter-0.8.5/dexter/R/data_selection.R | 66 ++ dexter-0.8.5/dexter/R/dexter.R | 240 +++++----- dexter-0.8.5/dexter/R/enorm.R | 18 dexter-0.8.5/dexter/R/equating.R | 2 dexter-0.8.5/dexter/R/misc.R | 35 + dexter-0.8.5/dexter/R/reparam.R | 12 dexter-0.8.5/dexter/build/vignette.rds |binary dexter-0.8.5/dexter/inst/doc/Equating.html | 25 - dexter-0.8.5/dexter/inst/doc/Plausible_Values.html | 43 - dexter-0.8.5/dexter/inst/doc/Test_Individual_differences.html | 19 dexter-0.8.5/dexter/inst/doc/data_management.R | 6 dexter-0.8.5/dexter/inst/doc/data_management.Rmd | 10 dexter-0.8.5/dexter/inst/doc/data_management.html | 20 dexter-0.8.5/dexter/inst/doc/dexter.html | 23 dexter-0.8.5/dexter/inst/doc/profile-plots.html | 25 - dexter-0.8.5/dexter/man/design_as_network.Rd | 36 - dexter-0.8.5/dexter/man/design_info.Rd |only dexter-0.8.5/dexter/man/fit_enorm.Rd | 3 dexter-0.8.5/dexter/vignettes/data_management.Rmd | 10 26 files changed, 401 insertions(+), 289 deletions(-)
Title: A Systematic Data Wrangling Idiom
Description: Supports systematic scrutiny, modification, and integration of
data. The function status() counts rows that have missing values in
grouping columns (returned by na() ), have non-unique combinations of
grouping columns (returned by dup() ), and that are not locally sorted
(returned by unsorted() ). Functions enumerate() and itemize() give
sorted unique combinations of columns, with or without occurrence counts,
respectively. Function ignore() drops columns in x that are present in y,
and informative() drops columns in x that are entirely NA; constant() returns
values that are constant, given a key. Data that have defined unique
combinations of grouping values behave more predictably during merge operations.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between wrangle versions 0.5.1 dated 2019-02-04 and 0.5.2 dated 2019-04-25
DESCRIPTION | 7 ++--- MD5 | 50 +++++++++++++++++++++--------------------- NAMESPACE | 4 +++ R/wrangle.R | 30 +++++++++++++++++++++++++ man/detect.Rd | 4 +++ man/dup.Rd | 2 + man/dup.grouped_df.Rd | 3 ++ man/dupGroups.Rd | 3 ++ man/dupGroups.grouped_df.Rd | 3 ++ man/enumerate.Rd | 4 +++ man/informative.Rd | 2 + man/informative.data.frame.Rd | 3 ++ man/itemize.Rd | 4 +++ man/key.Rd | 3 ++ man/key.grouped_df.Rd | 3 ++ man/na.Rd | 2 + man/na.grouped_df.Rd | 3 ++ man/naGroups.Rd | 3 ++ man/naGroups.grouped_df.Rd | 3 ++ man/static.Rd | 4 +++ man/status.Rd | 3 ++ man/status.grouped_df.Rd | 2 + man/unsorted.Rd | 2 + man/unsorted.grouped_df.Rd | 2 + man/weak.Rd | 2 + man/weak.grouped_df.Rd | 3 ++ 26 files changed, 125 insertions(+), 29 deletions(-)