Title: Improved Standard Evaluation Interfaces for Common Data
Manipulation Tasks
Description: The 'seplyr' (standard evaluation plying) package supplies improved
standard evaluation adapter methods for important common 'dplyr' data manipulation tasks.
In addition the 'seplyr' package supplies several new "key operations
bound together" methods. These include 'group_summarize()' (which
combines grouping, arranging and calculation in an atomic unit),
'add_group_summaries()' (which joins grouped summaries into a 'data.frame'
in a well documented manner), 'add_group_indices()' (which adds
per-group identifiers to a 'data.frame' without depending on row-order),
'partition_mutate_qt()' (which optimizes mutate sequences), and 'if_else_device()'
(which simulates per-row if-else blocks in expression sequences).
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between seplyr versions 0.5.1 dated 2018-01-03 and 0.5.2 dated 2018-01-20
seplyr-0.5.1/seplyr/man/expand_expr.Rd |only seplyr-0.5.1/seplyr/man/prep_deref.Rd |only seplyr-0.5.2/seplyr/DESCRIPTION | 13 -- seplyr-0.5.2/seplyr/MD5 | 39 +++--- seplyr-0.5.2/seplyr/NAMESPACE | 6 seplyr-0.5.2/seplyr/NEWS.md | 7 + seplyr-0.5.2/seplyr/R/package.R | 4 seplyr-0.5.2/seplyr/R/stmtPlanner.R | 99 +++++++++++++-- seplyr-0.5.2/seplyr/R/stringAlgebra.R | 8 - seplyr-0.5.2/seplyr/build/vignette.rds |binary seplyr-0.5.2/seplyr/inst/doc/MutatePartitioner.R | 56 +++++++- seplyr-0.5.2/seplyr/inst/doc/MutatePartitioner.Rmd | 60 ++++++++- seplyr-0.5.2/seplyr/inst/doc/MutatePartitioner.html | 130 ++++++++++++++++++-- seplyr-0.5.2/seplyr/inst/doc/factor_mutate.R |only seplyr-0.5.2/seplyr/inst/doc/factor_mutate.Rmd |only seplyr-0.5.2/seplyr/inst/doc/factor_mutate.html |only seplyr-0.5.2/seplyr/inst/doc/named_map_builder.html | 4 seplyr-0.5.2/seplyr/inst/doc/rename_se.html | 4 seplyr-0.5.2/seplyr/inst/doc/seplyr.html | 4 seplyr-0.5.2/seplyr/inst/doc/using_seplyr.html | 4 seplyr-0.5.2/seplyr/man/factor_mutate.Rd |only seplyr-0.5.2/seplyr/man/quote_mutate.Rd | 6 seplyr-0.5.2/seplyr/vignettes/MutatePartitioner.Rmd | 60 ++++++++- seplyr-0.5.2/seplyr/vignettes/factor_mutate.Rmd |only 24 files changed, 423 insertions(+), 81 deletions(-)
Title: Reliable Plying of Remote or Big Data with R
Description: Methods to use 'dplyr' remote data sources ('SQL' databases,
'Spark' 2.0.0 and above) in a reliable "generic" fashion (generic meaning
user code works similarly on all such sources, without needing per-source
adaption).
Adds convenience functions to make such tasks more like
working with an in-memory R 'data.frame'.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between replyr versions 0.9.0 dated 2017-11-12 and 0.9.1 dated 2018-01-20
replyr-0.9.0/replyr/R/tempNameGenerator.R |only replyr-0.9.0/replyr/inst/doc/FluidData.Rmd |only replyr-0.9.0/replyr/inst/doc/FluidData.html |only replyr-0.9.0/replyr/man/bind_rowsQ.Rd |only replyr-0.9.0/replyr/man/makeTempNameGenerator.Rd |only replyr-0.9.0/replyr/vignettes/FluidData.Rmd |only replyr-0.9.1/replyr/DESCRIPTION | 19 +-- replyr-0.9.1/replyr/MD5 | 88 +++++++--------- replyr-0.9.1/replyr/NAMESPACE | 6 - replyr-0.9.1/replyr/NEWS.md | 8 + replyr-0.9.1/replyr/R/addCol.R | 2 replyr-0.9.1/replyr/R/bind_rows.R | 110 ++------------------ replyr-0.9.1/replyr/R/checkRank.R | 2 replyr-0.9.1/replyr/R/coalesce.R | 2 replyr-0.9.1/replyr/R/expandColumn.R | 2 replyr-0.9.1/replyr/R/filter.R | 2 replyr-0.9.1/replyr/R/groupedApply.R | 2 replyr-0.9.1/replyr/R/inTest.R | 2 replyr-0.9.1/replyr/R/joinController.R | 2 replyr-0.9.1/replyr/R/land.R | 13 -- replyr-0.9.1/replyr/R/quantile.R | 4 replyr-0.9.1/replyr/R/replyr.R | 13 +- replyr-0.9.1/replyr/README.md | 84 +++++++++------ replyr-0.9.1/replyr/build/vignette.rds |binary replyr-0.9.1/replyr/inst/doc/DependencySorting.html | 103 ++++++++---------- replyr-0.9.1/replyr/inst/doc/NArm.html | 58 +++++----- replyr-0.9.1/replyr/inst/doc/ParametricExample.html | 4 replyr-0.9.1/replyr/inst/doc/coalesce.html | 41 ++++--- replyr-0.9.1/replyr/inst/doc/joinController.html | 109 +++++++++++-------- replyr-0.9.1/replyr/inst/doc/letExample.html | 28 ++--- replyr-0.9.1/replyr/inst/doc/replyr.Rmd | 19 +-- replyr-0.9.1/replyr/inst/doc/replyr.html | 36 +++--- replyr-0.9.1/replyr/inst/doc/summary.html | 12 +- replyr-0.9.1/replyr/man/addConstantColumn.Rd | 2 replyr-0.9.1/replyr/man/executeLeftJoinPlan.Rd | 2 replyr-0.9.1/replyr/man/expandColumn.Rd | 2 replyr-0.9.1/replyr/man/gapply.Rd | 2 replyr-0.9.1/replyr/man/grapes-land-grapes.Rd | 1 replyr-0.9.1/replyr/man/reexports.Rd | 4 replyr-0.9.1/replyr/man/replyr_bind_rows.Rd | 6 - replyr-0.9.1/replyr/man/replyr_check_ranks.Rd | 2 replyr-0.9.1/replyr/man/replyr_coalesce.Rd | 2 replyr-0.9.1/replyr/man/replyr_filter.Rd | 2 replyr-0.9.1/replyr/man/replyr_inTest.Rd | 2 replyr-0.9.1/replyr/man/replyr_quantile.Rd | 2 replyr-0.9.1/replyr/man/replyr_quantilec.Rd | 2 replyr-0.9.1/replyr/man/replyr_union_all.Rd | 2 replyr-0.9.1/replyr/vignettes/replyr.Rmd | 19 +-- 48 files changed, 388 insertions(+), 435 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient tree manipulations for large phylogenies, including pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism). Ancestral state reconstruction and hidden character prediction of discrete characters, using maximum likelihood and maximum parsimony methods. Simulating and fitting models of trait evolution, and generating random trees using birth-death models. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.3 dated 2017-11-29 and 1.3.2 dated 2018-01-20
DESCRIPTION | 12 MD5 | 36 NAMESPACE | 2 R/RcppExports.R | 28 R/asr_empirical_probabilities.R | 16 R/asr_mk_model.R | 5 R/asr_subtree_averaging.R |only R/generate_random_tree.R | 7 R/generate_tree_with_evolving_rates.R | 98 + R/get_subtree_with_tips.R | 4 R/hsp_subtree_averaging.R |only man/asr_mk_model.Rd | 9 man/asr_subtree_averaging.Rd |only man/generate_tree_with_evolving_rates.Rd | 112 + man/hsp_empirical_probabilities.Rd | 3 man/hsp_independent_contrasts.Rd | 4 man/hsp_max_parsimony.Rd | 3 man/hsp_mk_model.Rd | 2 man/hsp_subtree_averaging.Rd |only src/RcppExports.cpp | 163 +- src/phylogenetics_cpp_routines.cpp | 1905 ++++++++++++++++++------------- 21 files changed, 1501 insertions(+), 908 deletions(-)
Title: Escalation with Overdose Control
Description: An implementation of a variety of escalation with overdose control designs introduced by Babb, Rogatko and Zacks (1998) <doi:10.1002/(SICI)1097-0258(19980530)17:10%3C1103::AID-SIM793%3E3.0.CO;2-9>. It calculates the next dose as a clinical trial proceeds as well as performs simulations to obtain operating characteristics.
Author: Marcio A. Diniz <marcio.diniz@cshs.org>
Maintainer: Marcio A. Diniz <marcio.diniz@cshs.org>
Diff between ewoc versions 0.1.0 dated 2017-10-18 and 0.2.0 dated 2018-01-20
ewoc-0.1.0/ewoc/R/dpq_mtd.R |only ewoc-0.1.0/ewoc/R/simulation.R |only ewoc-0.1.0/ewoc/man/trial_simulation.Rd |only ewoc-0.2.0/ewoc/DESCRIPTION | 9 ++- ewoc-0.2.0/ewoc/MD5 | 51 +++++++++++----------- ewoc-0.2.0/ewoc/NAMESPACE | 23 ++++++--- ewoc-0.2.0/ewoc/NEWS.md |only ewoc-0.2.0/ewoc/R/classic_ewoc.R | 54 ++++++++++++++--------- ewoc-0.2.0/ewoc/R/extended_ewoc.R | 33 ++++++++------ ewoc-0.2.0/ewoc/R/next_dose.R | 33 ++++++++++++-- ewoc-0.2.0/ewoc/R/operating_characteristics.R | 60 +++++++++++++++----------- ewoc-0.2.0/ewoc/R/ph_ewoc.R | 46 ++++++++++++------- ewoc-0.2.0/ewoc/R/plot.R | 6 +- ewoc-0.2.0/ewoc/R/simulation_ewoc.R |only ewoc-0.2.0/ewoc/R/stop_rule.R | 10 ++-- ewoc-0.2.0/ewoc/R/utilities.R | 42 ++++++++++++++++-- ewoc-0.2.0/ewoc/README.md | 9 +-- ewoc-0.2.0/ewoc/man/dlt_rate.Rd | 10 ++-- ewoc-0.2.0/ewoc/man/ewoc_d1classic.Rd | 9 ++- ewoc-0.2.0/ewoc/man/ewoc_d1extended.Rd | 7 ++- ewoc-0.2.0/ewoc/man/ewoc_d1ph.Rd | 8 ++- ewoc-0.2.0/ewoc/man/ewoc_simulation.Rd |only ewoc-0.2.0/ewoc/man/inv_standard_dose.Rd |only ewoc-0.2.0/ewoc/man/logit.Rd |only ewoc-0.2.0/ewoc/man/mtd_bias.Rd | 10 ++-- ewoc-0.2.0/ewoc/man/mtd_mse.Rd | 10 ++-- ewoc-0.2.0/ewoc/man/optimal_mtd.Rd | 10 ++-- ewoc-0.2.0/ewoc/man/optimal_toxicity.Rd | 10 ++-- ewoc-0.2.0/ewoc/man/standard_dose.Rd |only ewoc-0.2.0/ewoc/man/stop_rule.Rd | 10 ++-- ewoc-0.2.0/ewoc/man/stop_rule_sim.Rd | 10 ++-- 31 files changed, 304 insertions(+), 166 deletions(-)
Title: Unpivot Complex and Irregular Data Layouts
Description: Tools for converting data from complex or irregular layouts to a
columnar structure. For example, tables with multilevel column or row
headers, or spreadsheets. Header and data cells are selected by their
contents and position, as well as formatting and comments where available,
and are associated with one other by their proximity in given directions.
Functions for data frames and HTML tables are provided.
Author: Duncan Garmonsway [aut, cre]
Maintainer: Duncan Garmonsway <nacnudus@gmail.com>
Diff between unpivotr versions 0.3.0 dated 2017-12-03 and 0.3.1 dated 2018-01-20
DESCRIPTION | 6 MD5 | 17 +- NEWS.md | 5 R/tidy_table.R | 24 +-- README.md | 34 ++-- inst/doc/compass-directions.html | 280 ++++++++++++++++++++------------------- inst/doc/html.html | 136 ++++++++++-------- inst/doc/small-multiples.html | 140 ++++++++++--------- man/figures |only man/tidy_table.Rd | 7 10 files changed, 342 insertions(+), 307 deletions(-)
Title: Tutorial Analysis of Some Agricultural Experiments
Description: Example software for the analysis of data from designed
experiments, especially agricultural crop experiments. The basics
of the statistical analysis of designed experiments are discussed
using real examples from agricultural field trials.
A range of statistical methods are exemplified using a range
of R statistical packages. The experimental
data is made available as separate data sets for each example
and the R analysis code is made available as example code.
The example code can be readily extended, as required.
Author: R. N. Edmondson and H.P. Piepho
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between agriTutorial versions 0.1.0 dated 2018-01-09 and 0.1.1 dated 2018-01-20
DESCRIPTION | 10 +++-- MD5 | 33 +++++++++------- NAMESPACE | 3 + R/agriTutorial-package.R | 2 - R/example1.R | 94 ++++++++++++++++++++++++++++++++++++++--------- R/example2.R | 3 - R/example3.R | 51 ++++++++++++++++++++++--- R/example4.R | 3 - R/example5.R | 3 - build |only inst |only man/agriTutorial.Rd | 2 - man/example1.Rd | 91 +++++++++++++++++++++++++++++++++++++-------- man/example2.Rd | 3 - man/example3.Rd | 51 ++++++++++++++++++++++--- man/example4.Rd | 3 - man/example5.Rd | 3 - vignettes |only 18 files changed, 273 insertions(+), 82 deletions(-)
Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner.
'vtreat' prepares variables so that data has fewer exceptional cases, making
it easier to safely use models in production. Common problems 'vtreat' defends
against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new
categorical levels (levels seen during application, but not during training).
'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 1.0.1 dated 2017-10-16 and 1.0.2 dated 2018-01-20
DESCRIPTION | 11 +-- MD5 | 58 ++++++++--------- NEWS.md | 126 +++++++++++++++++++------------------ R/outOfSample.R | 10 ++ R/utils.R | 11 ++- R/vtreat.R | 4 - R/zzz.R |only README.md | 20 ++--- build/vignette.rds |binary inst/doc/SavingTreamentPlans.Rmd | 2 inst/doc/SavingTreamentPlans.html | 11 +-- inst/doc/vtreat.html | 62 +++++++++--------- inst/doc/vtreatCrossFrames.Rmd | 2 inst/doc/vtreatCrossFrames.html | 128 +++++++++++++++++++------------------- inst/doc/vtreatGrouping.html | 32 ++++----- inst/doc/vtreatOverfit.html | 106 +++++++++++++++---------------- inst/doc/vtreatRareLevels.html | 70 ++++++++++---------- inst/doc/vtreatScaleMode.html | 52 +++++++-------- inst/doc/vtreatSignificance.html | 76 +++++++++++----------- inst/doc/vtreatSplitting.html | 66 +++++++++---------- inst/doc/vtreatVariableTypes.html | 82 ++++++++++++------------ man/prepare.Rd | 2 tests/testthat/testExpmtDesign.R | 34 ---------- tests/testthat/testExpmtDesign2.R |only tests/testthat/testNoY.R | 1 tests/testthat/testParallel.R | 9 +- tests/testthat/testUniqValue.R | 1 tests/testthat/testWeirdTypes.R | 2 tests/testthat/testZW.R | 1 vignettes/SavingTreamentPlans.Rmd | 2 vignettes/vtreatCrossFrames.Rmd | 2 31 files changed, 491 insertions(+), 492 deletions(-)
Title: Vectorised Tools for URL Handling and Parsing
Description: A toolkit for all URL-handling needs, including encoding and decoding,
parsing, parameter extraction and modification. All functions are
designed to be both fast and entirely vectorised. It is intended to be
useful for people dealing with web-related datasets, such as server-side
logs, although may be useful for other situations involving large sets of
URLs.
Author: Oliver Keyes [aut, cre], Jay Jacobs [aut, cre], Drew Schmidt [aut],
Mark Greenaway [ctb], Bob Rudis [ctb], Alex Pinto [ctb], Maryam Khezrzadeh [ctb], Peter Meilstrup [ctb],
Adam M. Costello [cph], Jeff Bezanson [cph], Peter Meilstrup [ctb], Xueyuan Jiang [ctb]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between urltools versions 1.6.0 dated 2016-10-16 and 1.7.0 dated 2018-01-20
urltools-1.6.0/urltools/src/accessors.cpp |only urltools-1.6.0/urltools/src/param.cpp |only urltools-1.6.0/urltools/src/urltools.cpp |only urltools-1.7.0/urltools/DESCRIPTION | 14 urltools-1.7.0/urltools/MD5 | 98 ++-- urltools-1.7.0/urltools/NAMESPACE | 5 urltools-1.7.0/urltools/NEWS | 33 + urltools-1.7.0/urltools/R/RcppExports.R | 302 ++++++++------ urltools-1.7.0/urltools/R/accessors.R | 71 ++- urltools-1.7.0/urltools/R/urltools.R | 12 urltools-1.7.0/urltools/README.md | 8 urltools-1.7.0/urltools/build/vignette.rds |binary urltools-1.7.0/urltools/inst/doc/urltools.Rmd | 2 urltools-1.7.0/urltools/inst/doc/urltools.html | 4 urltools-1.7.0/urltools/man/creds.Rd |only urltools-1.7.0/urltools/man/domain.Rd | 4 urltools-1.7.0/urltools/man/encoder.Rd | 1 urltools-1.7.0/urltools/man/fragment.Rd | 7 urltools-1.7.0/urltools/man/host_extract.Rd | 1 urltools-1.7.0/urltools/man/param_get.Rd | 11 urltools-1.7.0/urltools/man/param_remove.Rd | 1 urltools-1.7.0/urltools/man/param_set.Rd | 1 urltools-1.7.0/urltools/man/parameters.Rd | 12 urltools-1.7.0/urltools/man/path.Rd | 11 urltools-1.7.0/urltools/man/port.Rd | 11 urltools-1.7.0/urltools/man/puny.Rd | 3 urltools-1.7.0/urltools/man/scheme.Rd | 4 urltools-1.7.0/urltools/man/suffix_dataset.Rd | 1 urltools-1.7.0/urltools/man/suffix_extract.Rd | 1 urltools-1.7.0/urltools/man/suffix_refresh.Rd | 1 urltools-1.7.0/urltools/man/tld_dataset.Rd | 1 urltools-1.7.0/urltools/man/tld_extract.Rd | 1 urltools-1.7.0/urltools/man/tld_refresh.Rd | 1 urltools-1.7.0/urltools/man/url_compose.Rd | 1 urltools-1.7.0/urltools/man/url_parse.Rd | 6 urltools-1.7.0/urltools/man/urltools.Rd | 2 urltools-1.7.0/urltools/src/RcppExports.cpp | 221 +++++++--- urltools-1.7.0/urltools/src/compose.cpp | 27 + urltools-1.7.0/urltools/src/compose.h | 10 urltools-1.7.0/urltools/src/credentials.cpp |only urltools-1.7.0/urltools/src/encoding.cpp | 133 +++++- urltools-1.7.0/urltools/src/encoding.h | 12 urltools-1.7.0/urltools/src/parameter.cpp | 266 +++++++++++- urltools-1.7.0/urltools/src/parameter.h | 25 - urltools-1.7.0/urltools/src/parsing.cpp | 302 +++++++++++++- urltools-1.7.0/urltools/src/parsing.h | 229 +++++----- urltools-1.7.0/urltools/src/puny.cpp | 13 urltools-1.7.0/urltools/tests/testthat/test_credentials.R |only urltools-1.7.0/urltools/tests/testthat/test_encoding.R | 13 urltools-1.7.0/urltools/tests/testthat/test_get_set.R | 59 ++ urltools-1.7.0/urltools/tests/testthat/test_parameters.R | 37 + urltools-1.7.0/urltools/tests/testthat/test_parsing.R | 16 urltools-1.7.0/urltools/vignettes/urltools.Rmd | 2 53 files changed, 1469 insertions(+), 527 deletions(-)
Title: 3D Animated Interactive Visualizations Using SVG
Description: Creates 3D animated, interactive visualizations that can be viewed in a web browser.
Author: Aaron Olsen
Maintainer: Aaron Olsen <aarolsen@gmail.com>
Diff between svgViewR versions 1.2 dated 2016-09-26 and 1.3 dated 2018-01-20
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Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, vignettes, or function documentation. There is a shared object containing part of the 'CVODES' library, but it is not accessible from R. 'StanHeaders' is only useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut],
Trustees of Columbia University [cph],
Lawrence Livermore National Security [cph] (CVODES),
The Regents of the University of California [cph] (CVODES),
Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.17.1 dated 2017-12-20 and 2.17.2 dated 2018-01-20
DESCRIPTION | 8 MD5 | 34 +-- inst/include/src/stan/io/program_reader.hpp | 2 inst/include/src/stan/lang/rethrow_located.hpp | 2 inst/include/stan/math/mix/mat/functor/hessian.hpp | 4 inst/include/stan/math/prim/scal/fun/lb_constrain.hpp | 14 - inst/include/stan/math/prim/scal/fun/lb_free.hpp | 8 inst/include/stan/math/prim/scal/fun/lub_constrain.hpp | 20 - inst/include/stan/math/prim/scal/fun/lub_free.hpp | 12 - inst/include/stan/math/prim/scal/fun/ub_constrain.hpp | 16 - inst/include/stan/math/prim/scal/fun/ub_free.hpp | 8 inst/include/stan/math/rev/mat/fun/multiply.hpp | 144 ++++++------- inst/include/stan/math/rev/mat/fun/quad_form.hpp | 108 ++++----- inst/include/stan/math/rev/mat/fun/quad_form_sym.hpp | 34 +-- inst/include/stan/math/rev/mat/fun/trace_gen_quad_form.hpp | 90 ++++---- inst/include/stan/math/rev/mat/fun/trace_quad_form.hpp | 68 +++--- inst/include/stan/math/rev/mat/functor/algebra_solver.hpp | 26 +- inst/include/stan/math/rev/mat/functor/algebra_system.hpp | 8 18 files changed, 304 insertions(+), 302 deletions(-)
Title: Time-Frequency Analysis of 1-D Signals
Description: A set of R functions which provide an
environment for the Time-Frequency analysis of 1-D signals (and
especially for the wavelet and Gabor transforms of noisy
signals). It was originally written for Splus by Rene Carmona,
Bruno Torresani, and Wen L. Hwang, first at the University of
California at Irvine and then at Princeton University. Credit
should also be given to Andrea Wang whose functions on the
dyadic wavelet transform are included. Rwave is based on the
book: "Practical Time-Frequency Analysis: Gabor and Wavelet
Transforms with an Implementation in S", by Rene Carmona, Wen
L. Hwang and Bruno Torresani (1998, eBook ISBN:978008053942), Academic Press.
Author: Rene Carmona [aut],
Bruno Torresani [aut],
Brandon Whitcher [ctb],
Andrea Wang [ctb],
Wen-Liang Hwang [ctb],
Jonathan M. Lees [ctb, cre]
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between Rwave versions 2.4-5 dated 2017-03-21 and 2.4-8 dated 2018-01-20
Rwave-2.4-5/Rwave/man/Ekg.rd |only Rwave-2.4-5/Rwave/man/YN.rd |only Rwave-2.4-5/Rwave/man/YNdiff.rd |only Rwave-2.4-5/Rwave/man/amber7.rd |only Rwave-2.4-5/Rwave/man/amber8.rd |only Rwave-2.4-5/Rwave/man/amber9.rd |only Rwave-2.4-5/Rwave/man/b0.rd |only Rwave-2.4-5/Rwave/man/b4.rd |only Rwave-2.4-5/Rwave/man/c0.rd |only Rwave-2.4-5/Rwave/man/c4.rd |only Rwave-2.4-5/Rwave/man/cfamily.rd |only Rwave-2.4-5/Rwave/man/cgt.rd |only Rwave-2.4-5/Rwave/man/ch.rd |only Rwave-2.4-5/Rwave/man/cleanph.rd |only Rwave-2.4-5/Rwave/man/click.rd |only Rwave-2.4-5/Rwave/man/corona.rd |only Rwave-2.4-5/Rwave/man/coronoid.rd |only Rwave-2.4-5/Rwave/man/crc.rd |only Rwave-2.4-5/Rwave/man/crcrec.rd |only Rwave-2.4-5/Rwave/man/crfview.rd |only Rwave-2.4-5/Rwave/man/cwtimage.rd |only Rwave-2.4-5/Rwave/man/cwtp.rd |only Rwave-2.4-5/Rwave/man/cwtpolar.rd |only Rwave-2.4-5/Rwave/man/cwtsquiz.rd |only Rwave-2.4-5/Rwave/man/cwtth.rd |only Rwave-2.4-5/Rwave/man/d0.rd |only Rwave-2.4-5/Rwave/man/d4.rd |only Rwave-2.4-5/Rwave/man/dog.rd |only Rwave-2.4-5/Rwave/man/epl.rd |only Rwave-2.4-5/Rwave/man/ext.rd |only Rwave-2.4-5/Rwave/man/gabor.rd |only Rwave-2.4-5/Rwave/man/gcrcrec.rd |only Rwave-2.4-5/Rwave/man/gkernel.rd |only Rwave-2.4-5/Rwave/man/gregrec.rd |only Rwave-2.4-5/Rwave/man/gridrec.rd |only Rwave-2.4-5/Rwave/man/gwave.rd |only Rwave-2.4-5/Rwave/man/gwave2.rd |only Rwave-2.4-5/Rwave/man/icm.rd |only Rwave-2.4-5/Rwave/man/mbtrim.rd |only Rwave-2.4-5/Rwave/man/mntrim.rd |only Rwave-2.4-5/Rwave/man/morlet.rd |only Rwave-2.4-5/Rwave/man/morwave.rd |only Rwave-2.4-5/Rwave/man/morwave2.rd |only Rwave-2.4-5/Rwave/man/mrecons.rd |only Rwave-2.4-5/Rwave/man/mw.rd |only Rwave-2.4-5/Rwave/man/npl.rd |only Rwave-2.4-5/Rwave/man/plotwt.rd |only Rwave-2.4-5/Rwave/man/purwave.rd |only Rwave-2.4-5/Rwave/man/regrec.rd |only Rwave-2.4-5/Rwave/man/regrec2.rd |only Rwave-2.4-5/Rwave/man/ridrec.rd |only Rwave-2.4-5/Rwave/man/rkernel.rd |only Rwave-2.4-5/Rwave/man/rwkernel.rd |only Rwave-2.4-5/Rwave/man/scrcrec.rd |only Rwave-2.4-5/Rwave/man/skeleton.rd |only Rwave-2.4-5/Rwave/man/smoothts.rd |only Rwave-2.4-5/Rwave/man/smoothwt.rd |only Rwave-2.4-5/Rwave/man/snake.rd |only Rwave-2.4-5/Rwave/man/snakoid.rd |only Rwave-2.4-5/Rwave/man/sridrec.rd |only Rwave-2.4-5/Rwave/man/svd.rd |only Rwave-2.4-5/Rwave/man/tfgmax.rd |only Rwave-2.4-5/Rwave/man/tflmax.rd |only Rwave-2.4-5/Rwave/man/tfmean.rd |only Rwave-2.4-5/Rwave/man/tfpct.rd |only Rwave-2.4-5/Rwave/man/tfvar.rd |only Rwave-2.4-5/Rwave/man/vdog.rd |only Rwave-2.4-5/Rwave/man/vecgabor.rd |only Rwave-2.4-5/Rwave/man/vgt.rd |only Rwave-2.4-5/Rwave/man/vwt.rd |only Rwave-2.4-5/Rwave/man/wpl.rd |only Rwave-2.4-5/Rwave/man/wv.rd |only Rwave-2.4-8/Rwave/DESCRIPTION | 26 ++- Rwave-2.4-8/Rwave/MD5 | 233 ++++++++++++++--------------- Rwave-2.4-8/Rwave/inst |only Rwave-2.4-8/Rwave/man/DOG.Rd |only Rwave-2.4-8/Rwave/man/Ekg.Rd |only Rwave-2.4-8/Rwave/man/HOWAREYOU.Rd | 9 - Rwave-2.4-8/Rwave/man/HeartRate.Rd | 13 + Rwave-2.4-8/Rwave/man/SVD.Rd |only Rwave-2.4-8/Rwave/man/W_tilda.1.Rd | 10 + Rwave-2.4-8/Rwave/man/W_tilda.2.Rd | 10 + Rwave-2.4-8/Rwave/man/W_tilda.3.Rd | 9 - Rwave-2.4-8/Rwave/man/W_tilda.4.Rd | 9 - Rwave-2.4-8/Rwave/man/W_tilda.5.Rd | 9 - Rwave-2.4-8/Rwave/man/W_tilda.6.Rd | 10 + Rwave-2.4-8/Rwave/man/W_tilda.7.Rd | 9 - Rwave-2.4-8/Rwave/man/W_tilda.8.Rd | 11 + Rwave-2.4-8/Rwave/man/W_tilda.9.Rd | 11 + Rwave-2.4-8/Rwave/man/YN.Rd |only Rwave-2.4-8/Rwave/man/YNdiff.Rd |only Rwave-2.4-8/Rwave/man/a0.Rd | 9 - Rwave-2.4-8/Rwave/man/a4.Rd | 9 - Rwave-2.4-8/Rwave/man/amber7.Rd |only Rwave-2.4-8/Rwave/man/amber8.Rd |only Rwave-2.4-8/Rwave/man/amber9.Rd |only Rwave-2.4-8/Rwave/man/b0.Rd |only Rwave-2.4-8/Rwave/man/b4.Rd |only Rwave-2.4-8/Rwave/man/back1.000.Rd | 10 + Rwave-2.4-8/Rwave/man/back1.180.Rd | 10 + Rwave-2.4-8/Rwave/man/back1.220.Rd | 10 + Rwave-2.4-8/Rwave/man/backscatter.1.000.Rd | 10 + Rwave-2.4-8/Rwave/man/backscatter.1.180.Rd | 9 - Rwave-2.4-8/Rwave/man/backscatter.1.220.Rd | 11 + Rwave-2.4-8/Rwave/man/c0.Rd |only Rwave-2.4-8/Rwave/man/c4.Rd |only Rwave-2.4-8/Rwave/man/cfamily.Rd |only Rwave-2.4-8/Rwave/man/cgt.Rd |only Rwave-2.4-8/Rwave/man/ch.Rd |only Rwave-2.4-8/Rwave/man/chirpm5db.dat.Rd | 11 + Rwave-2.4-8/Rwave/man/cleanph.Rd |only Rwave-2.4-8/Rwave/man/click.Rd |only Rwave-2.4-8/Rwave/man/click.asc.Rd | 9 - Rwave-2.4-8/Rwave/man/corona.Rd |only Rwave-2.4-8/Rwave/man/coronoid.Rd |only Rwave-2.4-8/Rwave/man/crc.Rd |only Rwave-2.4-8/Rwave/man/crcrec.Rd |only Rwave-2.4-8/Rwave/man/crfview.Rd |only Rwave-2.4-8/Rwave/man/cwtimage.Rd |only Rwave-2.4-8/Rwave/man/cwtp.Rd |only Rwave-2.4-8/Rwave/man/cwtpolar.Rd |only Rwave-2.4-8/Rwave/man/cwtsquiz.Rd |only Rwave-2.4-8/Rwave/man/cwtth.Rd |only Rwave-2.4-8/Rwave/man/d0.Rd |only Rwave-2.4-8/Rwave/man/d4.Rd |only Rwave-2.4-8/Rwave/man/epl.Rd |only Rwave-2.4-8/Rwave/man/ext.Rd |only Rwave-2.4-8/Rwave/man/gabor.Rd |only Rwave-2.4-8/Rwave/man/gcrcrec.Rd |only Rwave-2.4-8/Rwave/man/gkernel.Rd |only Rwave-2.4-8/Rwave/man/gregrec.Rd |only Rwave-2.4-8/Rwave/man/gridrec.Rd |only Rwave-2.4-8/Rwave/man/gwave.Rd |only Rwave-2.4-8/Rwave/man/gwave2.Rd |only Rwave-2.4-8/Rwave/man/icm.Rd |only Rwave-2.4-8/Rwave/man/mbtrim.Rd |only Rwave-2.4-8/Rwave/man/mntrim.Rd |only Rwave-2.4-8/Rwave/man/morlet.Rd |only Rwave-2.4-8/Rwave/man/morwave.Rd |only Rwave-2.4-8/Rwave/man/morwave2.Rd |only Rwave-2.4-8/Rwave/man/mrecons.Rd |only Rwave-2.4-8/Rwave/man/mw.Rd |only Rwave-2.4-8/Rwave/man/noisy.dat.Rd | 9 - Rwave-2.4-8/Rwave/man/noisywave.Rd | 9 - Rwave-2.4-8/Rwave/man/npl.Rd |only Rwave-2.4-8/Rwave/man/pixel_8.7.Rd | 9 - Rwave-2.4-8/Rwave/man/pixel_8.8.Rd | 9 - Rwave-2.4-8/Rwave/man/pixel_8.9.Rd | 9 - Rwave-2.4-8/Rwave/man/plotwt.Rd |only Rwave-2.4-8/Rwave/man/pure.dat.Rd | 9 - Rwave-2.4-8/Rwave/man/purwave.Rd |only Rwave-2.4-8/Rwave/man/regrec.Rd |only Rwave-2.4-8/Rwave/man/regrec2.Rd |only Rwave-2.4-8/Rwave/man/ridrec.Rd |only Rwave-2.4-8/Rwave/man/rkernel.Rd |only Rwave-2.4-8/Rwave/man/rwkernel.Rd |only Rwave-2.4-8/Rwave/man/scrcrec.Rd |only Rwave-2.4-8/Rwave/man/sig_W_tilda.1.Rd | 9 - Rwave-2.4-8/Rwave/man/sig_W_tilda.2.Rd | 9 - Rwave-2.4-8/Rwave/man/sig_W_tilda.3.Rd | 9 - Rwave-2.4-8/Rwave/man/sig_W_tilda.4.Rd | 9 - Rwave-2.4-8/Rwave/man/sig_W_tilda.5.Rd | 9 - Rwave-2.4-8/Rwave/man/signal_W_tilda.1.Rd | 10 + Rwave-2.4-8/Rwave/man/signal_W_tilda.2.Rd | 8 Rwave-2.4-8/Rwave/man/signal_W_tilda.3.Rd | 9 - Rwave-2.4-8/Rwave/man/signal_W_tilda.4.Rd | 9 - Rwave-2.4-8/Rwave/man/signal_W_tilda.5.Rd | 9 - Rwave-2.4-8/Rwave/man/signal_W_tilda.6.Rd | 9 - Rwave-2.4-8/Rwave/man/signal_W_tilda.7.Rd | 9 - Rwave-2.4-8/Rwave/man/signal_W_tilda.8.Rd | 9 - Rwave-2.4-8/Rwave/man/signal_W_tilda.9.Rd | 10 + Rwave-2.4-8/Rwave/man/skeleton.Rd |only Rwave-2.4-8/Rwave/man/smoothts.Rd |only Rwave-2.4-8/Rwave/man/smoothwt.Rd |only Rwave-2.4-8/Rwave/man/snake.Rd |only Rwave-2.4-8/Rwave/man/snakoid.Rd |only Rwave-2.4-8/Rwave/man/sridrec.Rd |only Rwave-2.4-8/Rwave/man/tfgmax.Rd |only Rwave-2.4-8/Rwave/man/tflmax.Rd |only Rwave-2.4-8/Rwave/man/tfmean.Rd |only Rwave-2.4-8/Rwave/man/tfpct.Rd |only Rwave-2.4-8/Rwave/man/tfvar.Rd |only Rwave-2.4-8/Rwave/man/vdog.Rd |only Rwave-2.4-8/Rwave/man/vecgabor.Rd |only Rwave-2.4-8/Rwave/man/vgt.Rd |only Rwave-2.4-8/Rwave/man/vwt.Rd |only Rwave-2.4-8/Rwave/man/wpl.Rd |only Rwave-2.4-8/Rwave/man/wv.Rd |only Rwave-2.4-8/Rwave/man/yen.Rd | 11 + Rwave-2.4-8/Rwave/man/yendiff.Rd | 9 - 190 files changed, 501 insertions(+), 167 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided to parse, compile, test,
estimate, and analyze Stan models by accessing the header-only Stan library
provided by the 'StanHeaders' package. The Stan project develops a probabilistic
programming language that implements full Bayesian statistical inference
via Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
approximation, and (optionally penalized) maximum likelihood estimation via
optimization. In all three cases, automatic differentiation is used to quickly
and accurately evaluate gradients without burdening the user with the need to
derive the partial derivatives.
Author: Jiqiang Guo [aut],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Trustees of Columbia University [cph],
Oleg Sklyar [cph] (R/cxxfunplus.R),
The R Core Team [cph] (R/pairs.R, R/dynGet.R),
Jens Oehlschlaegel-Akiyoshi [cph] (R/pairs.R),
Hadley Wickham [cph] (R/rtools.R),
Joel de Guzman [cph] (Boost),
John Fletcher [cph] (Boost),
Thomas Heller [cph] (Boost),
Eric Niebler [cph] (Boost)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.17.2 dated 2017-12-20 and 2.17.3 dated 2018-01-20
DESCRIPTION | 12 +-- MD5 | 16 ++-- R/stanmodel-class.R | 45 +++++++---- build/vignette.rds |binary inst/NEWS | 9 ++ inst/doc/external.html | 18 ++-- inst/doc/rstan.html | 160 ++++++++++++++++++++-------------------- inst/doc/stanfit-objects.html | 168 +++++++++++++++++++++--------------------- src/Makevars | 5 + 9 files changed, 230 insertions(+), 203 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2017,
<doi:10.7287/peerj.preprints.3188v1>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou,
Nathan Russell, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.14 dated 2017-11-23 and 0.12.15 dated 2018-01-20
Rcpp-0.12.14/Rcpp/inst/unitTests/src/r-cran-testrcpppackage_0.1.0.orig.tar.gz |only Rcpp-0.12.15/Rcpp/ChangeLog | 133 + Rcpp-0.12.15/Rcpp/DESCRIPTION | 8 Rcpp-0.12.15/Rcpp/MD5 | 100 Rcpp-0.12.15/Rcpp/build/Rcpp.pdf |binary Rcpp-0.12.15/Rcpp/build/vignette.rds |binary Rcpp-0.12.15/Rcpp/inst/NEWS.Rd | 58 Rcpp-0.12.15/Rcpp/inst/bib/Rcpp.bib | 4 Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-FAQ.R | 2 Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-FAQ.Rmd | 2 Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-attributes.pdf |binary Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-extending.pdf |binary Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-introduction.pdf |binary Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-jss-2011.pdf |binary Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-modules.pdf |binary Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-package.pdf |binary Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-quickref.pdf |binary Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-sugar.pdf |binary Rcpp-0.12.15/Rcpp/inst/doc/Rcpp-unitTests.pdf |binary Rcpp-0.12.15/Rcpp/inst/doc/Rcpp.bib | 4 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/Environment.h | 47 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/Language.h | 12 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/RObject.h | 2 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/api/meat/DataFrame.h | 2 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/api/meat/Environment.h | 11 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/api/meat/Rcpp_eval.h | 101 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/api/meat/proxy.h | 18 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/config.h | 6 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/date_datetime/date_datetime.h | 4 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/exceptions.h | 21 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/exceptions/cpp11/exceptions.h | 2 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/exceptions/cpp98/exceptions.h | 40 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/internal/na.h | 63 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/internal/wrap.h | 3 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/macros/macros.h | 53 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/macros/unroll.h | 76 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/proxy/ProtectedProxy.h | 2 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/sugar/functions/is_na.h | 25 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/traits/is_na.h | 8 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/utils/tinyformat |only Rcpp-0.12.15/Rcpp/inst/include/Rcpp/utils/tinyformat.h | 1046 ---------- Rcpp-0.12.15/Rcpp/inst/include/Rcpp/vector/generic_proxy.h | 2 Rcpp-0.12.15/Rcpp/inst/include/Rcpp/vector/proxy.h | 10 Rcpp-0.12.15/Rcpp/inst/include/RcppCommon.h | 16 Rcpp-0.12.15/Rcpp/inst/unitTests/cpp/dates.cpp | 12 Rcpp-0.12.15/Rcpp/inst/unitTests/cpp/stack.cpp |only Rcpp-0.12.15/Rcpp/inst/unitTests/runit.Date.R | 14 Rcpp-0.12.15/Rcpp/inst/unitTests/runit.stack.R |only Rcpp-0.12.15/Rcpp/src/api.cpp | 6 Rcpp-0.12.15/Rcpp/src/attributes.cpp | 2 Rcpp-0.12.15/Rcpp/vignettes/Rcpp-FAQ.Rmd | 2 Rcpp-0.12.15/Rcpp/vignettes/Rcpp.bib | 4 53 files changed, 637 insertions(+), 1284 deletions(-)
Title: Acquisition and Processing of MODIS Products
Description: Download and processing functionalities for the Moderate Resolution
Imaging Spectroradiometer (MODIS). The package provides automated access to the
global online data archives LP DAAC (<https://lpdaac.usgs.gov/>) and LAADS
(<https://ladsweb.modaps.eosdis.nasa.gov/>) and processing capabilities such
as file conversion, mosaicking, subsetting and time series filtering.
Author: Matteo Mattiuzzi [aut],
Jan Verbesselt [ctb],
Tomislav Hengl [ctb],
Anja Klisch [ctb],
Forrest Stevens [ctb],
Steven Mosher [ctb],
Bradley Evans [ctb],
Agustin Lobo [ctb],
Koen Hufkens [ctb],
Florian Detsch [cre, aut]
Maintainer: Florian Detsch <fdetsch@web.de>
Diff between MODIS versions 1.1.0 dated 2017-07-03 and 1.1.1 dated 2018-01-20
MODIS-1.1.0/MODIS/inst/external/collections.rds |only MODIS-1.1.1/MODIS/DESCRIPTION | 22 MODIS-1.1.1/MODIS/LICENSE | 677 - MODIS-1.1.1/MODIS/MD5 | 112 MODIS-1.1.1/MODIS/NAMESPACE | 10 MODIS-1.1.1/MODIS/NEWS | 48 MODIS-1.1.1/MODIS/R/MODIS-package.R | 65 MODIS-1.1.1/MODIS/R/MODIS_QC.R | 456 MODIS-1.1.1/MODIS/R/MODISoptions.R | 962 + MODIS-1.1.1/MODIS/R/aaa-classes.R |only MODIS-1.1.1/MODIS/R/aggInterval.R | 246 MODIS-1.1.1/MODIS/R/arcStats.R | 561 - MODIS-1.1.1/MODIS/R/delHdf.R | 422 MODIS-1.1.1/MODIS/R/doOptions.R | 475 MODIS-1.1.1/MODIS/R/extractDate.R | 39 MODIS-1.1.1/MODIS/R/gdalControls.R | 320 MODIS-1.1.1/MODIS/R/genString.R | 35 MODIS-1.1.1/MODIS/R/getCollection.R | 55 MODIS-1.1.1/MODIS/R/getHdf.R | 769 - MODIS-1.1.1/MODIS/R/getPart.R | 11 MODIS-1.1.1/MODIS/R/getProduct.R | 112 MODIS-1.1.1/MODIS/R/getStruc.R | 486 - MODIS-1.1.1/MODIS/R/getTile.R | 586 - MODIS-1.1.1/MODIS/R/lpdaacLogin.R | 120 MODIS-1.1.1/MODIS/R/minorFuns.R | 1881 ++- MODIS-1.1.1/MODIS/R/miwhitatzb1.R | 341 MODIS-1.1.1/MODIS/R/orgStruc.R | 4 MODIS-1.1.1/MODIS/R/orgTime.R | 22 MODIS-1.1.1/MODIS/R/reformatDOY.R | 13 MODIS-1.1.1/MODIS/R/runGdal.R | 822 - MODIS-1.1.1/MODIS/R/runMrt.R | 718 - MODIS-1.1.1/MODIS/R/smoothSpline.R | 620 - MODIS-1.1.1/MODIS/R/temporalComposite.R | 210 MODIS-1.1.1/MODIS/R/transDate.R | 188 MODIS-1.1.1/MODIS/R/whittaker.R | 1057 +- MODIS-1.1.1/MODIS/R/zz_lazyload.R | 77 MODIS-1.1.1/MODIS/R/zzz.R | 44 MODIS-1.1.1/MODIS/README.md | 70 MODIS-1.1.1/MODIS/inst/external/LAADS_ftp.txt | 8698 +++++++++--------- MODIS-1.1.1/MODIS/inst/external/LPDAAC_ftp.txt | 8698 +++++++++--------- MODIS-1.1.1/MODIS/inst/external/MODIS_FTPinfo.RData |binary MODIS-1.1.1/MODIS/inst/external/MODIS_Opts.R | 88 MODIS-1.1.1/MODIS/inst/external/MODIS_Products.RData |binary MODIS-1.1.1/MODIS/inst/external/collections.RData |binary MODIS-1.1.1/MODIS/inst/external/modland_products.xlsx |only MODIS-1.1.1/MODIS/inst/external/tiletable.txt | 1304 +- MODIS-1.1.1/MODIS/man/MODISextent-class.Rd |only MODIS-1.1.1/MODIS/man/MODISoptions.Rd | 5 MODIS-1.1.1/MODIS/man/extractDate.Rd | 25 MODIS-1.1.1/MODIS/man/getCollection.Rd | 7 MODIS-1.1.1/MODIS/man/getHdf.Rd | 4 MODIS-1.1.1/MODIS/man/getProduct.Rd | 10 MODIS-1.1.1/MODIS/man/orgStruc.Rd | 2 MODIS-1.1.1/MODIS/man/orgTime.Rd | 10 MODIS-1.1.1/MODIS/man/reformatDOY.Rd | 13 MODIS-1.1.1/MODIS/man/temporalComposite.Rd | 4 MODIS-1.1.1/MODIS/man/whittaker.raster.Rd | 15 MODIS-1.1.1/MODIS/tests |only 58 files changed, 15481 insertions(+), 16058 deletions(-)
Title: Analysis of the 'Elements of Metacommunity Structure'
Description: Functions to analyze coherence, boundary clumping, and turnover
following the pattern-based metacommunity analysis of Leibold and Mikkelson
2002 <doi:10.1034/j.1600-0706.2002.970210.x>. The package also includes
functions to visualize ecological networks, and to calculate modularity
as a replacement to boundary clumping.
Author: Tad Dallas
Maintainer: Tad Dallas <tdallas@ucdavis.edu>
Diff between metacom versions 1.4.9 dated 2017-09-25 and 1.5.0 dated 2018-01-20
DESCRIPTION | 6 MD5 | 42 +++--- NAMESPACE | 44 +++---- NEWS.md | 4 R/BoundaryClump.R | 3 R/Coherence.R | 80 +++++++------ R/Metacommunity.R | 41 ++---- R/NullMaker.R | 97 +++++++++------ R/Turnover.R | 49 ++++++- man/BoundaryClump.Rd | 156 ++++++++++++------------- man/Coherence.Rd | 196 +++++++++++++++---------------- man/Imagine.Rd | 132 ++++++++++----------- man/Metacommunity.Rd | 221 ++++++++++++++++++------------------ man/Modularity.Rd | 184 ++++++++++++++--------------- man/NullMaker.Rd | 162 +++++++++++++------------- man/OrderMatrix.Rd | 138 +++++++++++----------- man/TestMatrices.Rd | 100 ++++++++-------- man/Turnover.Rd | 192 +++++++++++++++---------------- man/metacom-package.Rd | 176 ++++++++++++++-------------- tests/testthat/test-BoundaryClump.R | 4 tests/testthat/test-Coherence.R | 4 tests/testthat/test-Turnover.R | 8 - 22 files changed, 1044 insertions(+), 995 deletions(-)
Title: HTML Widgets for R
Description: A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents, and 'Shiny'
web applications.
Author: Ramnath Vaidyanathan [aut, cph],
Yihui Xie [aut],
JJ Allaire [aut, cre],
Joe Cheng [aut],
Kenton Russell [aut, cph],
RStudio [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between htmlwidgets versions 0.9 dated 2017-07-10 and 1.0 dated 2018-01-20
DESCRIPTION | 7 ++--- MD5 | 18 ++++++------ R/pandoc.R | 57 +++++++++++++++++++++++++++++++++++++++-- R/savewidget.R | 16 ++++++++--- R/widgetid.R | 5 ++- build/vignette.rds |binary inst/doc/develop_advanced.html | 4 +- inst/doc/develop_intro.html | 4 +- inst/doc/develop_sizing.html | 4 +- man/saveWidget.Rd | 4 ++ 10 files changed, 92 insertions(+), 27 deletions(-)
Title: Advanced Tables for Markdown/HTML
Description: Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While allowing
advanced layout, the underlying css-structure is simple in order to maximize
compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package
also contains a few text formatting functions that help outputting text
compatible with HTML/'LaTeX'.
Author: Max Gordon [aut, cre],
Stephen Gragg [aut],
Peter Konings [aut]
Maintainer: Max Gordon <max@gforge.se>
Diff between htmlTable versions 1.11.1 dated 2017-12-27 and 1.11.2 dated 2018-01-20
DESCRIPTION | 8 ++-- MD5 | 25 ++++++------- NEWS | 6 +++ R/htmlTable.R | 8 ++-- inst/doc/general.html | 70 ++++++++++++++++++------------------- inst/doc/tables.R | 5 +- inst/doc/tables.Rmd | 7 +-- inst/doc/tables.html | 71 ++++++++++++++++++-------------------- inst/doc/tidyHtmlTable.html | 24 ++++++------ man/htmlTable.Rd | 8 ++-- man/interactiveTable.Rd | 4 +- tests/testthat/test-htmlTable.R | 13 ++++-- tests/visual_tests/word_test.html |only vignettes/tables.Rmd | 7 +-- 14 files changed, 132 insertions(+), 124 deletions(-)
Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand-
alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and
available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to
show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical
method for visualizing high-dimensional data, in which a table of numbers
are encoded as a grid of colored cells. The rows and columns of the matrix
are ordered to highlight patterns and are often accompanied by 'dendrograms'.
'Heatmaps' are used in many fields for visualizing observations, correlations,
missing values patterns, and more. Interactive 'heatmaps' allow the inspection
of specific value by hovering the mouse over a cell, as well as zooming into
a region of the 'heatmap' by dragging a rectangle around the relevant area.
This work is based on the 'ggplot2' and 'plotly.js' engine. It produces
similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed
('plotly.js' is able to handle larger size matrix), the ability to zoom from
the 'dendrogram' panes, and the placing of factor variables in the sides of the
'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Jonathan Sidi [ctb] (https://github.com/yonicd),
Alan O'Callaghan [ctb] (https://github.com/Alanocallaghan),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between heatmaply versions 0.13.0 dated 2017-11-13 and 0.14.0 dated 2018-01-20
ChangeLog | 171 ++++++++++++ DESCRIPTION | 10 MD5 | 48 +-- NEWS | 40 ++ NEWS.md | 50 +++ R/RColorBrewer.R | 53 ++- R/distfuns.R | 3 R/heatmaply.R | 488 ++++++++++++++++++++--------------- R/heatmapr.R | 328 ++++++++++++----------- R/is.na10.R | 5 R/percentize.R | 27 - R/plots.R | 434 ++++++++++++++++++++----------- R/zzz.R | 51 ++- inst/doc/heatmaply.html | 72 ++--- man/heatmaply.Rd | 77 +++-- man/heatmapr.Rd | 15 - man/is.na10.Rd | 2 man/is.plotly.Rd | 2 tests/testthat.R | 1 tests/testthat/test_RColorBrewer.R | 58 ++-- tests/testthat/test_heatmaply.R | 100 ++++--- tests/testthat/test_heatmaply_misc.R | 67 +++- tests/testthat/test_heatmapr.R | 6 tests/testthat/test_misc.R | 10 tests/testthat/test_plots.R | 218 +++++++++------ 25 files changed, 1463 insertions(+), 873 deletions(-)
Title: Estimate Directed and Undirected Graphical Models and Construct
Networks
Description: Provides an equivalent measure of partial correlation coefficients for high-dimensional Gaussian Graphical Models to learn and visualize the underlying relationships between variables from single or multiple datasets. You can refer to Liang, F., Song, Q. and Qiu, P. (2015) <doi:10.1080/01621459.2015.1012391> for more detail. Based on this method, the package also provides the method for constructing networks for Next Generation Sequencing Data, for jointly estimating multiple Gaussian Graphical Models and constructing directed acyclic graph (Bayesian Network).
Author: Bochao Jia, Faming Liang, Runmin Shi, Suwa Xu
Maintainer: Bochao Jia <jbc409@ufl.edu>
Diff between equSA versions 1.1.4 dated 2018-01-10 and 1.1.5 dated 2018-01-20
DESCRIPTION | 8 MD5 | 18 - R/equSA.R | 21 - man/Cont2Gaus.Rd | 10 man/ContTran.Rd | 10 man/equSA-package.Rd | 21 - man/equSAR.Rd | 13 man/pcorselR.Rd | 58 +-- man/psical.Rd | 16 - src/equSA.c | 799 ++++++++++++++++++++++++++++----------------------- 10 files changed, 544 insertions(+), 430 deletions(-)
Title: Tools for Data Manipulation
Description: An implementation of common higher order functions with syntactic
sugar for anonymous function. Provides also a link to 'dplyr' for common
transformations on data frames to work around non standard evaluation by
default.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between dat versions 0.3.0 dated 2017-07-22 and 0.4.0 dated 2018-01-20
DESCRIPTION | 10 +-- LICENSE | 2 MD5 | 21 +++--- NEWS | 5 + R/deparse.R |only R/replace.R | 20 +----- build/vignette.rds |binary inst/doc/Introduction.html | 127 +++++++++++++++++++++--------------------- inst/doc/performance.html | 80 +++++++++++++------------- man/replace.Rd | 12 --- tests/testthat.R | 4 - tests/testthat/test-replace.R | 5 + 12 files changed, 144 insertions(+), 142 deletions(-)
Title: Fluid Data Transformations
Description: Supplies higher-order fluid data transform operators that include pivot and anti-pivot as special cases. Based on the 'DBI' database interface.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between cdata versions 0.5.1 dated 2018-01-04 and 0.5.2 dated 2018-01-20
cdata-0.5.1/cdata/R/bindRowsQ.R |only cdata-0.5.1/cdata/man/bind_rows_q.Rd |only cdata-0.5.2/cdata/DESCRIPTION | 10 +-- cdata-0.5.2/cdata/MD5 | 22 +++---- cdata-0.5.2/cdata/NAMESPACE | 1 cdata-0.5.2/cdata/NEWS.md | 4 + cdata-0.5.2/cdata/R/RowsColsQ.R | 106 ++++++++++++++++++++++++---------- cdata-0.5.2/cdata/R/old_fns.R | 36 +++++------ cdata-0.5.2/cdata/README.md | 6 - cdata-0.5.2/cdata/inst/doc/cdata.R | 6 + cdata-0.5.2/cdata/inst/doc/cdata.Rmd | 21 +++++- cdata-0.5.2/cdata/inst/doc/cdata.html | 20 ++++-- cdata-0.5.2/cdata/vignettes/cdata.Rmd | 21 +++++- 13 files changed, 173 insertions(+), 80 deletions(-)
Title: A 'DBI' Interface to the 'Yandex Clickhouse' Database Providing
Basic 'dplyr' Support
Description: 'Yandex Clickhouse' (<https://clickhouse.yandex/>) is a high-performance relational column-store database to enable
big data exploration and 'analytics' scaling to petabytes of data. Methods are
provided that enable working with 'Yandex Clickhouse' databases via
'DBI' methods and using 'dplyr'/'dbplyr' idioms.
Author: Christian Hotz-Behofsits [aut, cre],
Clemens Danninger [aut],
Simon Stiebellehner [aut],
Dan Egnor [aut],
Vlad Losev [aut],
Keith Ray [aut],
Zhanyong Wan [aut],
Markus Heule [aut],
Google [cph],
Yann Collet [cph]
Maintainer: Christian Hotz-Behofsits <christian.hotz-behofsits@wu.ac.at>
Diff between RClickhouse versions 0.3.0 dated 2017-11-26 and 0.4.0 dated 2018-01-20
RClickhouse-0.3.0/RClickhouse/inst/include/clckhs.h |only RClickhouse-0.4.0/RClickhouse/DESCRIPTION | 19 + RClickhouse-0.4.0/RClickhouse/MD5 | 60 +++-- RClickhouse-0.4.0/RClickhouse/NAMESPACE | 2 RClickhouse-0.4.0/RClickhouse/R/ClickhouseDriver.R | 63 +++++- RClickhouse-0.4.0/RClickhouse/R/RcppExports.R | 26 +- RClickhouse-0.4.0/RClickhouse/R/dbplyr-helpers.R |only RClickhouse-0.4.0/RClickhouse/R/dplyr.R | 37 ++- RClickhouse-0.4.0/RClickhouse/inst/CITATION |only RClickhouse-0.4.0/RClickhouse/inst/include/RClickhouse_RcppExports.h |only RClickhouse-0.4.0/RClickhouse/man/ClickhouseDriver-class.Rd | 16 + RClickhouse-0.4.0/RClickhouse/man/sql_variant.Rd |only RClickhouse-0.4.0/RClickhouse/src/Makevars.common | 3 RClickhouse-0.4.0/RClickhouse/src/RClickhouse_init.c | 54 ++--- RClickhouse-0.4.0/RClickhouse/src/RcppExports.cpp | 102 +++++----- RClickhouse-0.4.0/RClickhouse/src/connection.cpp | 55 +++++ RClickhouse-0.4.0/RClickhouse/src/result.cpp | 38 +++ RClickhouse-0.4.0/RClickhouse/src/vendor/clickhouse-cpp/clickhouse/CMakeLists.txt | 1 RClickhouse-0.4.0/RClickhouse/src/vendor/clickhouse-cpp/clickhouse/client.cpp | 2 RClickhouse-0.4.0/RClickhouse/src/vendor/clickhouse-cpp/clickhouse/client.h | 1 RClickhouse-0.4.0/RClickhouse/src/vendor/clickhouse-cpp/clickhouse/columns/factory.cpp | 4 RClickhouse-0.4.0/RClickhouse/src/vendor/clickhouse-cpp/clickhouse/columns/nullable.cpp | 4 RClickhouse-0.4.0/RClickhouse/src/vendor/clickhouse-cpp/clickhouse/columns/uuid.cpp |only RClickhouse-0.4.0/RClickhouse/src/vendor/clickhouse-cpp/clickhouse/columns/uuid.h |only RClickhouse-0.4.0/RClickhouse/src/vendor/clickhouse-cpp/clickhouse/types/types.cpp | 14 + RClickhouse-0.4.0/RClickhouse/src/vendor/clickhouse-cpp/clickhouse/types/types.h | 15 + RClickhouse-0.4.0/RClickhouse/src/vendor/clickhouse-cpp/ut/columns_ut.cpp | 46 ++++ RClickhouse-0.4.0/RClickhouse/src/vendor/clickhouse-cpp/ut/types_ut.cpp | 6 RClickhouse-0.4.0/RClickhouse/tests/testthat.R | 3 RClickhouse-0.4.0/RClickhouse/tests/testthat/fixture_config.yaml |only RClickhouse-0.4.0/RClickhouse/tests/testthat/test-agg.R |only RClickhouse-0.4.0/RClickhouse/tests/testthat/test-array.R | 34 --- RClickhouse-0.4.0/RClickhouse/tests/testthat/test-config.R |only RClickhouse-0.4.0/RClickhouse/tests/testthat/test-enum.R |only RClickhouse-0.4.0/RClickhouse/tests/testthat/test-regr-15.R | 18 - RClickhouse-0.4.0/RClickhouse/tests/testthat/test-regr-25.R |only RClickhouse-0.4.0/RClickhouse/tests/testthat/test-uuid.R |only RClickhouse-0.4.0/RClickhouse/tests/testthat/utils.R |only 38 files changed, 432 insertions(+), 191 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.5 dated 2017-10-08 and 0.6 dated 2018-01-20
DESCRIPTION | 10 MD5 | 23 NAMESPACE | 14 NEWS | 4 R/ICA.BinCont.R | 470 ++++++++- R/SPF.BinCont.R |only R/Summary.SPF.BinCont.R |only R/plot.PPE.BinBin.R | 2 R/plot.SPPBinCont.R |only R/plot_SPPBinBin.R | 2495 ++++++++++++++++++++++++------------------------ man/ICABinCont.Rd | 29 man/SPP.BinCont.Rd |only man/plot.SPPBinBin.Rd | 112 +- man/plot.SPPBinCont.Rd |only man/summary.gen.Rd | 2 15 files changed, 1807 insertions(+), 1354 deletions(-)
Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'.
Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions,
conditioned scatter plot with marginal densities,
box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between WVPlots versions 0.2.7 dated 2017-11-28 and 0.2.8 dated 2018-01-20
DESCRIPTION | 12 ++++++------ MD5 | 21 ++++++++++++--------- NAMESPACE | 5 +++++ NEWS.md | 10 ++++++++-- R/FitHistoryPlot.R |only R/GainCurve.R | 8 ++++---- R/WVPlots.R | 8 ++++++++ README.md | 6 ++++++ build/vignette.rds |binary inst/doc/WVPlots_concept.html | 4 ++-- inst/doc/WVPlots_examples.html | 4 ++-- man/plot_Keras_fit_trajectory.Rd |only man/plot_fit_trajectory.Rd |only 13 files changed, 53 insertions(+), 25 deletions(-)