Title: Portable System Utilities
Description: Powerful replacements for base system2 with consistent behavior
across platforms. Supports interruption, background tasks, and full control over
STDOUT / STDERR binary or text streams. On Unix systems the package also has
functions for evaluating expressions inside a temporary fork. Such evaluations
have no side effects on the main R process, and support reliable interrupts and
timeouts. This provides the basis for a sandboxing mechanism.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Gábor Csárdi [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between sys versions 1.5 dated 2017-10-10 and 1.6 dated 2018-07-24
DESCRIPTION | 21 ++++++------ MD5 | 25 ++++++++------ NEWS | 3 + R/exec.R | 4 +- R/fork.R | 12 ++++--- inst |only man/eval_fork.Rd | 1 man/exec.Rd | 4 +- src/Makevars.win | 2 - src/fork.c | 72 ++++++++++++++++++++++++++---------------- src/init.c |only src/util.c | 5 -- src/win32/exec.c | 7 +++- tests/spelling.R |only tests/testthat/test-forking.R | 13 +++++++ 15 files changed, 107 insertions(+), 62 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of Höhle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available monitoring procedures is
given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>.
For the retrospective analysis of epidemic spread, the package provides
three endemic-epidemic modeling frameworks with tools for visualization,
likelihood inference, and simulation. 'hhh4' estimates models for
(multivariate) count time series following Paul and Held (2011)
<doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>.
'twinSIR' models the susceptible-infectious-recovered (SIR) event
history of a fixed population, e.g, epidemics across farms or networks,
as a multivariate point process as proposed by Höhle (2009)
<doi:10.1002/bimj.200900050>. 'twinstim' estimates self-exciting point
process models for a spatio-temporal point pattern of infective events,
e.g., time-stamped geo-referenced surveillance data, as proposed by
Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>.
A recent overview of the implemented space-time modeling frameworks
for epidemic phenomena is given by Meyer et al. (2017)
<doi:10.18637/jss.v077.i11>.
Author: Michael Höhle [aut, ths] (<https://orcid.org/0000-0002-0423-6702>),
Sebastian Meyer [aut, cre] (<https://orcid.org/0000-0002-1791-9449>),
Michaela Paul [aut],
Leonhard Held [ctb, ths],
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Andrea Riebler [ctb],
Daniel Sabanés Bové [ctb],
Maëlle Salmon [ctb],
Dirk Schumacher [ctb],
Stefan Steiner [ctb],
Mikko Virtanen [ctb],
Wei Wei [ctb],
Valentin Wimmer [ctb],
R Core Team [ctb] (A few code segments are modified versions of code
from base R)
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.16.1 dated 2018-05-28 and 1.16.2 dated 2018-07-24
DESCRIPTION | 10 MD5 | 73 NAMESPACE | 2 R/catCUSUM.R | 17 R/fanplot.R | 30 R/hhh4_plot.R | 30 R/hhh4_simulate.R | 23 R/spatial_tools.R | 43 R/sts_ggplot.R | 10 R/twinstim_simulation.R | 7 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 34 inst/doc/glrnb.pdf |binary inst/doc/hhh4.pdf |binary inst/doc/hhh4_spacetime.R | 32 inst/doc/hhh4_spacetime.Rnw | 71 inst/doc/hhh4_spacetime.pdf |binary inst/doc/monitoringCounts.R | 59 inst/doc/monitoringCounts.Rnw | 3614 ++++++++++----------- inst/doc/monitoringCounts.pdf |binary inst/doc/surveillance.pdf |binary inst/doc/twinSIR.pdf |binary inst/doc/twinstim.pdf | 52 man/algo.hhh.grid.Rd | 2 man/backprojNP.Rd | 4 man/boda.Rd | 7 man/categoricalCUSUM.Rd | 2 man/fanplot.Rd | 10 man/sts_ggplot.Rd | 6 tests/testthat/test-hhh4_offsets.R |only vignettes/hhh4_spacetime.Rnw | 71 vignettes/monitoringCounts-cache/boda.RData |binary vignettes/monitoringCounts-cache/boda.covars.RData |binary vignettes/monitoringCounts.Rnw | 3614 ++++++++++----------- vignettes/references.bib | 13 vignettes/surveillance-cache.RData |binary vignettes/surveillance-hmm.pdf |binary 38 files changed, 4006 insertions(+), 3830 deletions(-)
Title: Class and Methods for Hyperspectral Data
Description: Input/Output, processing and visualization of spectra taken with different spectrometers, including SVC (Spectra Vista), ASD and PSR (Spectral Evolution). Implements an S3 class 'spectra' that other packages can build on. Provides methods to access, plot, manipulate, splice sensor overlap, vector normalize and smooth spectra.
Author: Jose Eduardo Meireles [aut, cre],
Anna K. Schweiger [aut],
Jeannine Cavender-Bares [aut]
Maintainer: Jose Eduardo Meireles <meireles@umn.edu>
Diff between spectrolab versions 0.0.6 dated 2018-06-19 and 0.0.7 dated 2018-07-24
DESCRIPTION | 10 ++-- MD5 | 28 ++++++----- NEWS.md | 20 +++++--- R/getters_and_setters.R | 80 ++++++++++++++++++++++++++------ R/read_spectra.R | 13 ----- R/stats_function_overloads.R | 12 ++++ build/vignette.rds |binary inst/doc/advanced_spectrolab.pdf |binary inst/doc/introduction_to_spectrolab.pdf |binary inst/doc/match_sensors.pdf |binary man/i_read_ascii_spectra.Rd | 5 -- man/i_read_asd_spectra.Rd | 5 -- man/quantile.spectra.Rd | 5 +- man/read_spectra.Rd | 6 -- tests/testthat/test_quantile_name.R |only tests/testthat/test_spec_setter.R |only 16 files changed, 120 insertions(+), 64 deletions(-)
Title: Fits a Principal Curve in Arbitrary Dimension
Description: Fitting a principal curve to a data matrix in arbitrary dimensions.
Author: Trevor Hastie [aut],
Andreas Weingessel [aut],
Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>),
Henrik Bengtsson [ctb] (HenrikBengtsson),
Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between princurve versions 2.1.1 dated 2018-07-23 and 2.1.2 dated 2018-07-24
princurve-2.1.1/princurve/inst/doc/algorithm.R |only princurve-2.1.1/princurve/inst/doc/algorithm.Rmd |only princurve-2.1.1/princurve/inst/doc/algorithm.html |only princurve-2.1.1/princurve/inst/doc/benchmarks.R |only princurve-2.1.1/princurve/inst/doc/benchmarks.Rmd |only princurve-2.1.1/princurve/inst/doc/benchmarks.html |only princurve-2.1.1/princurve/man/figures/README_compare-1.png |only princurve-2.1.1/princurve/man/figures/README_example_data-1.png |only princurve-2.1.1/princurve/man/figures/README_example_plot-1.png |only princurve-2.1.1/princurve/vignettes/algorithm.Rmd |only princurve-2.1.1/princurve/vignettes/benchmarks.Rmd |only princurve-2.1.2/princurve/DESCRIPTION | 16 + princurve-2.1.2/princurve/MD5 | 38 +--- princurve-2.1.2/princurve/R/get.lam.R | 6 princurve-2.1.2/princurve/R/principal.curve.R | 22 +- princurve-2.1.2/princurve/R/principal_curve.R | 16 + princurve-2.1.2/princurve/README.md | 82 +--------- princurve-2.1.2/princurve/build/vignette.rds |binary princurve-2.1.2/princurve/inst/NEWS | 9 + princurve-2.1.2/princurve/inst/doc/intro.R |only princurve-2.1.2/princurve/inst/doc/intro.Rmd |only princurve-2.1.2/princurve/inst/doc/intro.html |only princurve-2.1.2/princurve/man/figures/README_example-1.gif |only princurve-2.1.2/princurve/man/principal_curve.Rd | 11 - princurve-2.1.2/princurve/tests/testthat/test-legacy_princurve.R | 26 ++- princurve-2.1.2/princurve/tests/testthat/test-principal_curve.R | 10 - princurve-2.1.2/princurve/tests/testthat/test-project_to_curve.R | 14 - princurve-2.1.2/princurve/vignettes/intro.Rmd |only 28 files changed, 114 insertions(+), 136 deletions(-)
Title: Piecewise Structural Equation Modeling
Description: Implements piecewise structural equation modeling from a single
list of structural equations, with new methods for non-linear, latent, and
composite variables, standardized coefficients, query-based prediction and
indirect effects. See <http://jslefche.github.io/piecewiseSEM/> for more.
Author: Jon Lefcheck [aut, cre],
Jarrett Byrnes [aut],
James Grace [aut]
Maintainer: Jon Lefcheck <jlefcheck@bigelow.org>
Diff between piecewiseSEM versions 2.0.1 dated 2018-07-03 and 2.0.2 dated 2018-07-24
DESCRIPTION | 8 - MD5 | 22 ++--- NEWS.md | 4 R/coefs.R | 12 +- R/partialResid.R | 6 - R/piecewiseSEM-package.R | 2 R/psem.R | 2 R/rsquared.R | 18 ++-- R/zzz.R | 2 README.md | 5 - inst/doc/piecewiseSEM.html | 186 +++++++++++++++++++------------------------- man/piecewiseSEM-package.Rd | 2 12 files changed, 127 insertions(+), 142 deletions(-)
Title: Visualization using Graph Traversal
Description: Improving graphics by ameliorating order effects, using Eulerian tours and Hamiltonian decompositions of graphs.
Author: C.B. Hurley and R.W. Oldford
Maintainer: Catherine Hurley <catherine.hurley@mu.ie>
Diff between PairViz versions 1.2.1 dated 2011-12-09 and 1.3.1 dated 2018-07-24
PairViz-1.2.1/PairViz/data/cancer.txt.gz |only PairViz-1.3.1/PairViz/DESCRIPTION | 22 +++---- PairViz-1.3.1/PairViz/MD5 | 49 +++++++++------ PairViz-1.3.1/PairViz/NAMESPACE | 7 +- PairViz-1.3.1/PairViz/R/eseq.R | 52 ++++++++++------ PairViz-1.3.1/PairViz/R/hamorder.R | 34 ++++++++-- PairViz-1.3.1/PairViz/R/mcplot.R | 88 ++++++++++++++++++++-------- PairViz-1.3.1/PairViz/R/specialg.R | 63 +++++++++++++++++--- PairViz-1.3.1/PairViz/build |only PairViz-1.3.1/PairViz/data/cancer.txt |only PairViz-1.3.1/PairViz/demo/nav.R | 93 +++++++++++++++++++----------- PairViz-1.3.1/PairViz/demo/stepwise.R | 96 +++++++++++++++++++++---------- PairViz-1.3.1/PairViz/inst |only PairViz-1.3.1/PairViz/man/eseq.Rd | 15 ++-- PairViz-1.3.1/PairViz/man/etour.Rd | 3 PairViz-1.3.1/PairViz/man/hpaths.Rd | 6 + PairViz-1.3.1/PairViz/man/mc_plot.Rd | 11 +-- PairViz-1.3.1/PairViz/man/order_best.Rd | 5 - PairViz-1.3.1/PairViz/man/order_tsp.Rd | 2 PairViz-1.3.1/PairViz/man/overlayci.Rd | 4 - PairViz-1.3.1/PairViz/man/overview.Rd | 8 +- PairViz-1.3.1/PairViz/man/pcp.Rd | 9 ++ PairViz-1.3.1/PairViz/man/tableplot.Rd | 19 ++++-- PairViz-1.3.1/PairViz/man/whpaths.Rd | 3 PairViz-1.3.1/PairViz/vignettes |only 25 files changed, 405 insertions(+), 184 deletions(-)
Title: Non-Homogeneous Markov Switching Autoregressive Models
Description: Calibration, simulation, validation of (non-)homogeneous Markov switching autoregressive models with Gaussian or von Mises innovations. Penalization methods are implemented for Markov Switching Vector Autoregressive Models of order 1 only. Most functions of the package handle missing values.
Author: Valerie Monbet
Maintainer: Valerie Monbet <valerie.monbet@gmail.com>
Diff between NHMSAR versions 1.9 dated 2018-07-22 and 1.10 dated 2018-07-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/Mstep.hh.MSAR.R | 16 +++++++++++----- R/fit.MSAR.R | 3 ++- man/Mstep.hh.MSAR.Rd | 5 ++++- 5 files changed, 24 insertions(+), 14 deletions(-)
Title: Compute Krippendorff's Alpha
Description: Provides functions to compute and plot Krippendorff's inter-coder
reliability coefficient alpha and bootstrapped uncertainty estimates
(Krippendorff 2004, ISBN:0761915443). The bootstrap routines are set up to
make use of parallel threads where supported.
Author: Alexander Staudt [aut, cre], Pierre L'Ecuyer [ctb] (author of the C++ RNG code)
Maintainer: Alexander Staudt <staudtlex@live.de>
Diff between icr versions 0.5.5 dated 2018-07-23 and 0.5.6 dated 2018-07-24
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- configure | 43 +++++++++++++++++++++++++++++++++---------- configure.ac | 2 +- 4 files changed, 41 insertions(+), 18 deletions(-)
Title: Finding Rhythms Using Extended Circadian Harmonic Oscillators
(ECHO)
Description: Provides a function (echo_find()) designed to find rhythms
from data using extended harmonic oscillators. For more information,
see H. De los Santos et al. (2017) <doi:10.1145/3107411.3107420> .
Author: Hannah De los Santos [aut, cre],
Emily Collins [aut],
Jonathan Shewchuk [ctb],
E.F. Harding [ctb],
Kristin Bennett [aut],
Jennifer Hurley [aut]
Maintainer: Hannah De los Santos <delosh@rpi.edu>
Diff between echo.find versions 1.1.1 dated 2018-06-21 and 1.2.1 dated 2018-07-24
DESCRIPTION | 6 MD5 | 8 R/echo_utils.R | 359 +++++++++++++++++++++++++++----------------- inst/CITATION | 4 inst/doc/echo-vignette.html | 6 5 files changed, 239 insertions(+), 144 deletions(-)
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison, Tom Drake, Riinu Ots
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 0.8.1 dated 2018-07-17 and 0.8.2 dated 2018-07-24
DESCRIPTION | 13 - MD5 | 43 +++-- NAMESPACE | 19 ++ NEWS | 9 + R/boot_predict.R | 2 R/ff_glimpse.R | 28 +-- R/ff_mcar.R |only R/ff_merge.R | 1 R/ff_missing.R | 13 + R/ff_newdata.R | 1 R/finalfit_internal_functions.R | 291 +++++++++++++++++++++++++++++++++++++++- R/finalfit_package.R | 4 R/fit2df_glm.R | 4 R/fit2df_glmlist.R | 4 R/metrics_hoslem.R |only R/missing_plot.R |only README.md | 13 + inst/doc/finalfit_basics.html | 6 man/ff_describe.Rd |only man/ff_mcar.Rd |only man/ff_missing.Rd | 4 man/interp.median.Rd |only man/interp.quantiles.Rd |only man/kurtosi.Rd |only man/metrics_hoslem.Rd |only man/missing_plot.Rd |only man/plot_title.Rd | 2 man/skew.Rd |only 28 files changed, 400 insertions(+), 57 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as getting database specific taxonomic identifiers, verifying
species names, getting taxonomic hierarchies, fetching downstream and
upstream taxonomic names, getting taxonomic synonyms, converting
scientific to common names and vice versa, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Eduard Szoecs [aut],
Zachary Foster [aut],
Zebulun Arendsee [aut],
Carl Boettiger [ctb],
Karthik Ram [ctb],
Ignasi Bartomeus [ctb],
John Baumgartner [ctb],
James O'Donnell [ctb],
Jari Oksanen [ctb],
Bastian Greshake Tzovaras [ctb],
Philippe Marchand [ctb],
Vinh Tran [ctb],
Maëlle Salmon [ctb],
Gaopeng Li [ctb],
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.9.3 dated 2018-03-20 and 0.9.4 dated 2018-07-24
DESCRIPTION | 83 +++++++++++++++++------- MD5 | 93 +++++++++++++-------------- NAMESPACE | 5 + NEWS.md | 26 +++++++ R/class2tree.R | 9 +- R/classification.R | 7 -- R/col_search.R | 8 +- R/comm2sci.R | 4 - R/gbif_downstream.R | 25 ++++++- R/genbank2uid.R | 9 -- R/get_boldid.R | 15 +++- R/get_uid.R | 17 +--- R/getkey.R | 53 ++++----------- R/gnr_datasources.R | 6 + R/gnr_resolve.R | 2 R/key_helpers.R |only R/nbn_search.R | 4 - R/ncbi_children.R | 22 ++---- R/ncbi_get_taxon_summary.R | 43 ++++++++---- R/ping.R | 22 ++++-- R/sci2comm.R | 7 -- R/synonyms.R | 33 +++++---- R/tax_name.R | 2 R/tp_refs.R | 2 R/tp_search.R | 11 --- R/tp_summary.R | 8 +- R/zzz.R | 10 ++ README.md | 88 +++++++++++++------------ build/vignette.rds |binary man/gbif_downstream.Rd | 12 +++ man/getkey.Rd | 42 +----------- man/key_helpers.Rd |only man/tp_refs.Rd | 2 man/tp_summary.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-class2tree.R | 5 + tests/testthat/test-classification.R | 4 - tests/testthat/test-downstream.R | 2 tests/testthat/test-gbif_downstream.R | 6 - tests/testthat/test-get_boldid.R | 9 ++ tests/testthat/test-iucn_id.R | 6 - tests/testthat/test-iucn_summary.R | 16 ++-- tests/testthat/test-key_helpers.R |only tests/testthat/test-ncbi_get_taxon_summary.R | 4 - tests/testthat/test-ping.R | 1 tests/testthat/test-tax_name.R | 33 +++++---- tests/testthat/test-tp_accnames.R | 2 tests/testthat/test-tp_search.R | 2 tests/testthat/test-tp_summary.R | 2 49 files changed, 429 insertions(+), 335 deletions(-)
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression as described for example
in Hundepol et al. (2012) <doi:10.1002/9781118348239> are covered in this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@gmail.com>
Diff between sdcTable versions 0.23 dated 2018-06-22 and 0.24 dated 2018-07-24
DESCRIPTION | 8 - MD5 | 18 +- build/vignette.rds |binary data/microData1.RData |binary data/microData2.RData |binary data/problem.RData |binary data/problemWithSupps.RData |binary data/protectedData.RData |binary inst/doc/sdcTable.html | 22 +- src/suppMultDimTable.cpp | 328 +++++++++++++++++++++++++------------------- 10 files changed, 210 insertions(+), 166 deletions(-)
Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional
disaggregated indicators. So far, estimation methods comprise direct estimation
and the model-based approach Empirical Best Prediction (see "Small area
estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>),
as well as their precision estimates. The assessment of the used model
is supported by a summary and diagnostic plots. For a suitable presentation of
estimates, map plots can be easily created. Furthermore, results can easily be
exported to excel.
Author: Ann-Kristin Kreutzmann [aut],
Soeren Pannier [aut, cre],
Natalia Rojas-Perilla [aut],
Timo Schmid [aut],
Matthias Templ [aut],
Nikos Tzavidis [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>
Diff between emdi versions 1.1.2 dated 2018-04-04 and 1.1.3 dated 2018-07-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/compare.R | 26 +++++++++++++++++--------- R/summary.emdi.R | 9 +++++++-- inst/doc/vignette_emdi.pdf |binary 6 files changed, 39 insertions(+), 20 deletions(-)
Title: Bayesian Inference for the Multivariate Skew-t Model
Description: Estimates the multivariate skew-t and nested models, as described in the
articles Liseo, B., Parisi, A. (2013). Bayesian inference for the multivariate skew-normal
model: a population Monte Carlo approach. Comput. Statist. Data Anal.
<doi:10.1016/j.csda.2013.02.007> and in Parisi, A., Liseo, B. (2017). Objective Bayesian
analysis for the multivariate skew-t model. Statistical Methods & Applications
<doi: 10.1007/s10260-017-0404-0>.
Author: Antonio Parisi [aut, cre],
Brunero Liseo [aut],
Dirk Eddelbuettel [ctb],
Romain Francois [ctb]
Maintainer: Antonio Parisi <antonio.parisi@uniroma2.it>
Diff between mvst versions 1.0.1 dated 2016-07-25 and 1.1.0 dated 2018-07-24
mvst-1.0.1/mvst/R/modelParTypes.R |only mvst-1.0.1/mvst/src/rvST.c |only mvst-1.0.1/mvst/src/rvT.c |only mvst-1.1.0/mvst/DESCRIPTION | 28 +++--- mvst-1.1.0/mvst/MD5 | 146 ++++++++++++++++++-------------- mvst-1.1.0/mvst/NAMESPACE | 15 ++- mvst-1.1.0/mvst/R/MNmargLike.R |only mvst-1.1.0/mvst/R/MTmargLike.R |only mvst-1.1.0/mvst/R/WUiterations.R | 43 +++++---- mvst-1.1.0/mvst/R/bivPlot.R |only mvst-1.1.0/mvst/R/cmlN.R | 59 ++++++++---- mvst-1.1.0/mvst/R/cmlSE.R | 14 +-- mvst-1.1.0/mvst/R/cmlSN.R | 89 +++++++++++++------ mvst-1.1.0/mvst/R/cmlST.R | 101 ++++++++++++++-------- mvst-1.1.0/mvst/R/cmlT.R | 75 +++++++++++----- mvst-1.1.0/mvst/R/coef.mcSEsummary.R |only mvst-1.1.0/mvst/R/dmvSE.R |only mvst-1.1.0/mvst/R/estListInit.R | 19 +++- mvst-1.1.0/mvst/R/estListUpdate.R | 29 +++--- mvst-1.1.0/mvst/R/initialPointsN.R | 34 ++++++- mvst-1.1.0/mvst/R/initialPointsSN.R | 90 ++++++++++++++----- mvst-1.1.0/mvst/R/initialPointsST.R | 61 ++++++++++--- mvst-1.1.0/mvst/R/initialPointsT.R | 61 ++++++++----- mvst-1.1.0/mvst/R/iterEstimates.R | 106 +++++++++++++++-------- mvst-1.1.0/mvst/R/iterations.R | 55 ++++++------ mvst-1.1.0/mvst/R/logPostDensN.R | 42 ++++++--- mvst-1.1.0/mvst/R/logPostDensSN.R | 42 ++++++--- mvst-1.1.0/mvst/R/logPostDensST.R | 40 ++++++-- mvst-1.1.0/mvst/R/logPostDensT.R | 53 +++++++---- mvst-1.1.0/mvst/R/logPriorDensN.R | 10 +- mvst-1.1.0/mvst/R/logPriorDensSN.R | 13 -- mvst-1.1.0/mvst/R/logPriorDensST.R | 17 +-- mvst-1.1.0/mvst/R/logPriorDensT.R | 15 +-- mvst-1.1.0/mvst/R/mcSE.R | 76 ++++++++++------ mvst-1.1.0/mvst/R/modelParInfo.R |only mvst-1.1.0/mvst/R/print.summary.mcSE.R | 7 - mvst-1.1.0/mvst/R/reparamSkew.R | 3 mvst-1.1.0/mvst/R/reparamT.R | 7 - mvst-1.1.0/mvst/R/rmvSE.R | 87 ++++++++++++------- mvst-1.1.0/mvst/R/sampleBN.R |only mvst-1.1.0/mvst/R/sampleBSN.R |only mvst-1.1.0/mvst/R/sampleBST.R |only mvst-1.1.0/mvst/R/sampleBT.R |only mvst-1.1.0/mvst/R/sampleBtrue.R |only mvst-1.1.0/mvst/R/sampleGN.R | 51 +++++++++-- mvst-1.1.0/mvst/R/sampleGSN.R | 42 ++++++--- mvst-1.1.0/mvst/R/sampleGST.R | 68 ++++++-------- mvst-1.1.0/mvst/R/sampleGT.R | 44 ++++++--- mvst-1.1.0/mvst/R/sampleGtrue.R | 5 - mvst-1.1.0/mvst/R/samplenuST.R | 5 - mvst-1.1.0/mvst/R/samplenuT.R | 7 - mvst-1.1.0/mvst/R/samplenutrue.R | 3 mvst-1.1.0/mvst/R/samplepsiSN.R | 39 +++++--- mvst-1.1.0/mvst/R/samplepsiST.R | 61 +++++-------- mvst-1.1.0/mvst/R/samplepsitrue.R | 5 - mvst-1.1.0/mvst/R/samplevST.R | 25 ++--- mvst-1.1.0/mvst/R/samplevT.R | 25 +++-- mvst-1.1.0/mvst/R/samplevtrue.R | 3 mvst-1.1.0/mvst/R/samplexiN.R | 3 mvst-1.1.0/mvst/R/samplexiSN.R | 7 - mvst-1.1.0/mvst/R/samplexiST.R | 77 ++++++++-------- mvst-1.1.0/mvst/R/samplexiT.R | 15 +-- mvst-1.1.0/mvst/R/samplexitrue.R | 5 - mvst-1.1.0/mvst/R/samplezSN.R | 28 +++--- mvst-1.1.0/mvst/R/samplezST.R | 28 +++--- mvst-1.1.0/mvst/R/sampleztrue.R | 3 mvst-1.1.0/mvst/R/summary.mcSE.R | 97 +++++++++++---------- mvst-1.1.0/mvst/R/villaPrior.R |only mvst-1.1.0/mvst/build |only mvst-1.1.0/mvst/configure | 32 ++++--- mvst-1.1.0/mvst/configure.ac | 2 mvst-1.1.0/mvst/man/MNmargLike.Rd |only mvst-1.1.0/mvst/man/bivPlot.Rd |only mvst-1.1.0/mvst/man/cmlSE.Rd | 23 ++--- mvst-1.1.0/mvst/man/coef.mcSEsummary.Rd |only mvst-1.1.0/mvst/man/dmvSE.Rd |only mvst-1.1.0/mvst/man/mcSE.Rd | 42 ++++----- mvst-1.1.0/mvst/man/mvst-package.Rd | 22 +--- mvst-1.1.0/mvst/man/rmvSE.Rd | 23 ++--- mvst-1.1.0/mvst/man/summary.mcSE.Rd |only mvst-1.1.0/mvst/src/mvst_init.c |only mvst-1.1.0/mvst/src/rvSTs.c |only mvst-1.1.0/mvst/src/rvTs.c |only mvst-1.1.0/mvst/src/rzSN.c | 49 +++++----- mvst-1.1.0/mvst/src/rzSNX.c |only mvst-1.1.0/mvst/src/rzST.c | 49 +++++----- mvst-1.1.0/mvst/src/rzSTX.c |only 87 files changed, 1427 insertions(+), 898 deletions(-)
Title: Compute High Dimensional Orthant Probabilities
Description: Computationally efficient method to estimate orthant probabilities of high-dimensional Gaussian vectors. Further implements a function to compute conservative estimates of excursion sets under Gaussian random field priors.
Author: Dario Azzimonti
Maintainer: Dario Azzimonti <dario.azzimonti@gmail.com>
Diff between anMC versions 0.2.0 dated 2017-11-21 and 0.2.1 dated 2018-07-24
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- NEWS.md | 8 +++++++- R/ANMC0_2.R | 2 +- R/ConsEstv0_6.R | 11 +++++++---- R/MC0_2.R | 2 +- R/ProbaMax.R | 2 +- R/ProbaMin.R | 2 +- R/help.R | 6 +++--- R/optimizeEq.R | 4 ++-- README.md | 6 +++--- man/ANMC_Gauss.Rd | 2 +- man/MC_Gauss.Rd | 2 +- man/ProbaMax.Rd | 2 +- man/ProbaMin.Rd | 2 +- man/anMC.Rd | 6 +++--- man/conservativeEstimate.Rd | 9 ++++++--- man/selectActiveDims.Rd | 2 +- man/selectQdims.Rd | 2 +- src/tmvrnorm_rej2.cpp | 2 +- 20 files changed, 65 insertions(+), 53 deletions(-)
Title: Control the Number of Threads on 'BLAS'
Description: Control the number of threads on 'BLAS' (Aka 'GotoBLAS', 'OpenBLAS', 'ACML', 'BLIS' and 'MKL').
And possible to control the number of threads in 'OpenMP'.
Get a number of logical cores and physical cores if feasible.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama <nakama@ki.rim.or.jp>
Maintainer: Ei-ji Nakama <nakama@ki.rim.or.jp>
Diff between RhpcBLASctl versions 0.18-185 dated 2018-07-05 and 0.18-205 dated 2018-07-24
ChangeLog | 6 + DESCRIPTION | 10 +-- MD5 | 14 ++-- R/blasctl.R | 20 +++--- README | 6 + man/RhpcBLASctl-package.Rd | 4 + src/blasctl.c | 141 ++++++++++++++++++++------------------------- src/blasctl.h | 27 +++++++- 8 files changed, 126 insertions(+), 102 deletions(-)
Title: Exploratory Regression 'Shiny' App
Description: Constructs a 'shiny' app function with interactive displays for summary and analysis of variance regression tables, and parallel coordinate plots of data and residuals.
Author: Catherine B. Hurley
Maintainer: Catherine B. Hurley <catherine.hurley@mu.ie>
Diff between ERSA versions 0.1.0 dated 2018-04-05 and 0.1.1 dated 2018-07-24
DESCRIPTION | 11 +++++----- MD5 | 14 +++++++------ NAMESPACE | 3 ++ R/appPlots.R | 7 +++--- R/helper.R | 53 ++++++++++++++++++++++++++++++++++------------------ build/vignette.rds |binary inst/doc/ERSA.html | 4 +-- man/add1_models.Rd |only man/drop1_models.Rd |only 9 files changed, 58 insertions(+), 34 deletions(-)
Title: Quality Control Metrics for Gene Signatures
Description: Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics.
Author: Andrew Dhawan [aut],
Alessandro Barberis [aut],
Wei-Chen Cheng [aut],
Francesca Buffa [aut, cre]
Maintainer: Francesca Buffa <francesca.buffa@oncology.ox.ac.uk>
Diff between sigQC versions 0.1.20 dated 2018-06-13 and 0.1.21 dated 2018-07-24
DESCRIPTION | 7 LICENSE | 675 ++++++++++++++++++++++++++++++++++++++++++++++- MD5 | 16 - R/eval_compactness_loc.R | 8 R/make_all_plots.R | 2 R/make_radar_chart_loc.R | 2 inst/doc/vignette.Rmd | 12 inst/doc/vignette.html | 18 - vignettes/vignette.Rmd | 12 9 files changed, 713 insertions(+), 39 deletions(-)
Title: Permits *apply() Style Dispatch for 'HPC'
Description: Function of apply style using 'MPI' provides better 'HPC' environment on R.
And this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO <nakanoj@ism.ac.jp> and Ei-ji Nakama <nakama@ki.rim.or.jp>
Maintainer: Ei-ji Nakama <nakama@ki.rim.or.jp>
Diff between Rhpc versions 0.18-185 dated 2018-07-05 and 0.18-204 dated 2018-07-24
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- README | 5 +++-- src/RhpcSerialize.c | 6 +++--- src/worker/RhpcWorker_Lapplyseq.h | 2 +- 6 files changed, 21 insertions(+), 15 deletions(-)
Title: Encrypt and Decrypt Strings, R Objects and Files
Description: A consistent interface to encrypt and decrypt strings, R objects and files using symmetric and asymmetric key encryption.
Author: KS Srikanth [aut, cre]
Maintainer: KS Srikanth <sri.teach@gmail.com>
Diff between safer versions 0.2.0 dated 2017-10-30 and 0.2.1 dated 2018-07-24
DESCRIPTION | 8 +++--- MD5 | 12 +++++----- NEWS.md | 3 ++ R/string.R | 59 +++++++++++++++++++++++++++++++++++--------------- README.md | 11 ++++++--- man/decrypt_string.Rd | 16 +++++++++---- man/encrypt_string.Rd | 21 ++++++++++++----- 7 files changed, 89 insertions(+), 41 deletions(-)
Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS)
implemented by the MICE algorithm as described in Van Buuren and
Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has
its own imputation model. Built-in imputation models are provided for
continuous data (predictive mean matching, normal), binary data (logistic
regression), unordered categorical data (polytomous logistic regression)
and ordered categorical data (proportional odds). MICE can also impute
continuous two-level data (normal model, pan, second-level variables).
Passive imputation can be used to maintain consistency between variables.
Various diagnostic plots are available to inspect the quality of the
imputations.
Author: Stef van Buuren [aut, cre],
Karin Groothuis-Oudshoorn [aut],
Alexander Robitzsch [ctb],
Gerko Vink [ctb],
Lisa Doove [ctb],
Shahab Jolani [ctb],
Rianne Schouten [ctb],
Philipp Gaffert [ctb],
Florian Meinfelder [ctb],
Bernie Gray [ctb]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between mice versions 3.1.0 dated 2018-06-20 and 3.2.0 dated 2018-07-24
mice-3.1.0/mice/tests/testthat/Rplots.pdf |only mice-3.2.0/mice/DESCRIPTION | 8 +- mice-3.2.0/mice/MD5 | 32 ++++---- mice-3.2.0/mice/NEWS.md |only mice-3.2.0/mice/R/barnard.rubin.R | 2 mice-3.2.0/mice/R/generics.R | 4 - mice-3.2.0/mice/R/md.pattern.R | 10 +- mice-3.2.0/mice/R/method.R | 2 mice-3.2.0/mice/R/mice.impute.2l.norm.R | 2 mice-3.2.0/mice/R/parlmice.R | 44 ++++++++--- mice-3.2.0/mice/R/pool.R | 27 +++++- mice-3.2.0/mice/man/parlmice.Rd | 20 ++--- mice-3.2.0/mice/man/pool.Rd | 9 ++ mice-3.2.0/mice/tests/testthat/test-D1.R | 29 ++++--- mice-3.2.0/mice/tests/testthat/test-cbind.R | 4 - mice-3.2.0/mice/tests/testthat/test-mice.impute.2l.norm.R | 10 +- mice-3.2.0/mice/tests/testthat/test-parlmice.R | 55 +++++++++----- mice-3.2.0/mice/tests/testthat/test-rbind.R | 4 + 18 files changed, 168 insertions(+), 94 deletions(-)
Title: Spatial Inference using Integrated Nested Laplace Approximation
Description: Facilitates spatial modeling using integrated nested Laplace approximation via the
INLA package (<http://www.r-inla.org>). Additionally, implements a log Gaussian Cox process likelihood for
modeling univariate and spatial point processes based on ecological survey data. See Yuan Yuan,
Fabian E. Bachl, Finn Lindgren, David L. Borchers, Janine B. Illian, Stephen T. Buckland, Havard Rue,
Tim Gerrodette (2017), <arXiv:1604.06013>.
Author: Fabian E. Bachl [aut, cre] (Fabian Bachl wrote the main code),
Finn Lindgren [aut] (<https://orcid.org/0000-0002-5833-2011>, Finn
Lindgren wrote code for SPDE posterior plotting, and continued
development of the main code),
David L. Borchers [ctb] (David Borchers wrote code for Gorilla data
import and sampling, multiplot tool),
Daniel Simpson [ctb] (Daniel Simpson wrote the basic LGCP sampling
method),
Lindesay Scott-Howard [ctb] (Lindesay Scott-Howard provied MRSea data
import code)
Maintainer: Fabian E. Bachl <bachlfab@gmail.com>
Diff between inlabru versions 2.1.3 dated 2018-02-11 and 2.1.9 dated 2018-07-24
DESCRIPTION | 48 +- MD5 | 156 ++++---- NAMESPACE | 6 NEWS.md |only R/bru.gof.R | 1 R/bru.inference.R | 257 +++++++++---- R/bru.integration.R | 40 +- R/covariate.R | 10 R/data.gorillas.R | 2 R/data.mexdolphin.R | 1 R/environment.R | 19 - R/ggplot.R | 21 - R/inla.R | 238 ++++++++---- R/inlabru.R | 3 R/integration.R | 293 +++++++++++++-- R/mesh.R | 8 R/model.R | 13 R/nlinla.R | 15 R/plotsample.R | 21 - R/rgl.R | 4 R/sampling.R | 611 +++++++++++++++++++++++---------- R/stack.R | 31 + README.md |only data/Poisson1_1D.RData |binary data/Poisson2_1D.RData |binary data/Poisson3_1D.RData |binary data/mexdolphin.RData |binary data/mrsea.RData |binary data/seals.RData |binary data/toygroups.RData |binary inst/examples/bru.R | 18 inst/examples/devel.cvmeasure.R | 10 inst/examples/generate.bru.R | 4 inst/examples/gg.inla.mesh.R | 2 inst/examples/gg.spatial.R | 2 inst/examples/gmap.R | 4 inst/examples/like.R | 5 inst/examples/predict.bru.R | 12 inst/examples/rgl.R | 9 inst/examples/spde.posterior.R | 9 man/bincount.Rd | 1 man/bru.Rd | 29 + man/bru.options.Rd | 14 man/cprod.Rd | 4 man/devel.cvmeasure.Rd | 10 man/generate.Rd | 7 man/generate.bru.Rd | 17 man/generate.inla.Rd |only man/gg.RasterLayer.Rd | 9 man/gg.Rd | 2 man/gg.SpatialGridDataFrame.Rd | 2 man/gg.SpatialLines.Rd | 2 man/gg.SpatialPixelsDataFrame.Rd | 2 man/gg.SpatialPoints.Rd | 2 man/gg.SpatialPolygons.Rd | 2 man/gg.inla.mesh.1d.Rd | 7 man/gg.inla.mesh.Rd | 2 man/globe.Rd | 12 man/glplot.Rd | 9 man/glplot.SpatialLines.Rd | 9 man/glplot.SpatialPoints.Rd | 9 man/glplot.inla.mesh.Rd | 9 man/gm.Rd | 4 man/gmap.Rd | 7 man/gorillas.Rd | 2 man/init.tutorial.Rd | 4 man/int.Rd | 6 man/int.polygon.Rd |only man/integration_weight_construction.Rd |only man/intersection_mesh.Rd |only man/ipoints.Rd | 8 man/is.inside.Rd | 7 man/lgcp.Rd | 13 man/like.Rd | 18 man/make_stable_integration_points.Rd |only man/plotsample.Rd | 8 man/point2count.Rd | 9 man/predict.bru.Rd | 12 man/predict.inla.Rd | 20 - man/sample.lgcp.Rd | 86 +++- man/spde.posterior.Rd | 9 man/split_lines.Rd |only man/summary.bru.Rd | 18 83 files changed, 1578 insertions(+), 686 deletions(-)
Title: Satellite Nightlight Data Extraction
Description: Extracts raster and zonal statistics
from satellite nightlight rasters downloaded from the United States
National Oceanic and Atmospheric Administration (<http://www.noaa.gov>)
free data repositories. Both the DMSP-OLS annual and SNPP-VIIRS monthly
nightlight raster data are supported. Satellite nightlight raster tiles are
downloaded and cropped to the country boundaries using shapefiles from the GADM
database of Global Administrative Areas (<http://gadm.org>). Zonal statistics
are then calculated at the lowest administrative boundary for the selected
country and cached locally for future retrieval. Finally, a simple data
explorer/browser is included that allows one to visualize the cached data e.g.
graphing, mapping and clustering regional data.
Author: Christopher Njuguna [aut, cre, cph]
Maintainer: Christopher Njuguna <chris.njuguna@gmail.com>
Diff between Rnightlights versions 0.2.1 dated 2018-05-26 and 0.2.2 dated 2018-07-24
DESCRIPTION | 20 MD5 | 120 ++-- NAMESPACE | 1 R/ctrycode.R | 84 +++ R/ctrynldata.R | 473 ++++++++++++++---- R/getnlfilename.R | 12 R/nightlights.R | 280 +++++++---- R/nlperiod.R | 91 +-- R/nltype.R | 2 R/options.R | 4 R/polygons.R | 904 +++++++++++++++++++++++++++++------- R/stats.R | 77 ++- R/upgrade.R | 30 - inst/application/server.R | 50 + inst/application/ui.R | 14 man/ZonalPipe.Rd | 7 man/addCtryPolyIdx.Rd |only man/allValidCtryAdmLvls.Rd | 7 man/createCtryNlDataDF.Rd | 7 man/createCtryStruct.Rd | 7 man/ctryShpLyrName2Num.Rd | 13 man/deleteNlDataCol.Rd | 9 man/dnldCtryPoly.Rd | 9 man/existsCtryNlData.Rd | 7 man/existsCtryNlDataFile.Rd | 7 man/existsCtryPoly.Rd |only man/existsPolyFnamePath.Rd | 7 man/existsPolyFnameZip.Rd | 7 man/fnAggRadGdal.Rd | 9 man/fnAggRadRast.Rd | 6 man/getAllGadmVersions.Rd |only man/getCtryNlData.Rd | 19 man/getCtryNlDataFname.Rd | 7 man/getCtryNlDataFnamePath.Rd | 7 man/getCtryPolyAdmLevelNames.Rd | 8 man/getCtryPolyUrl.Rd | 7 man/getCtryRasterOutputFname.Rd | 8 man/getCtryRasterOutputFnamePath.Rd | 8 man/getCtryShpAllAdmLvls.Rd | 7 man/getCtryShpLowestLyrNames.Rd | 7 man/getCtryShpLyrNames.Rd | 7 man/getCtryStructAdmLevelNames.Rd |only man/getCtryStructFname.Rd | 7 man/getCtryStructFnamePath.Rd | 7 man/getPolyFname.Rd | 7 man/getPolyFnamePath.Rd | 7 man/getPolyFnameRDS.Rd |only man/getPolyFnameZip.Rd | 7 man/listCtryNlData.Rd | 15 man/listCtryNlRasters.Rd | 8 man/listNlTiles.Rd | 5 man/orderCustPolyLayers.Rd |only man/processNLCountry.Rd | 14 man/processNlData.Rd | 16 man/readCtryPolyAdmLayer.Rd | 7 man/readCtryStruct.Rd | 7 man/saveCtryNlData.Rd | 7 man/searchAdmLevel.Rd | 14 man/searchCountry.Rd |only man/validCtryAdmLvls.Rd | 7 man/validGadmVersions.Rd |only tests/testthat.R | 2 tests/testthat/test-admlevels.R | 12 tests/testthat/test-nlfilename.R | 29 - tests/testthat/test-nlperiods.R | 4 65 files changed, 1930 insertions(+), 601 deletions(-)
Title: Pseudo-Ranks
Description: Efficient calculation of pseudo-ranks. In case of equal sample sizes, pseudo-ranks and mid-ranks are equal. When used for inference mid-ranks may lead to paradoxical results. Pseudo-ranks are in general not affected by such a problem. For details, see Brunner, E., Bathke A. C. and Konietschke, F: Rank- and Pseudo-Rank Procedures in Factorial Designs - Using R and SAS, Springer Verlag, to appear.
Author: Martin Happ [aut, cre] (<https://orcid.org/0000-0003-0009-2665>),
Georg Zimmermann [aut],
Arne C. Bathke [aut],
Edgar Brunner [aut]
Maintainer: Martin Happ <martin.happ@aon.at>
Diff between pseudorank versions 0.2.5 dated 2018-07-23 and 0.2.6 dated 2018-07-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/pseudorank.cpp | 4 +++- 3 files changed, 9 insertions(+), 7 deletions(-)
Title: Computing Log-Transformed Kernel Density Estimates for Positive
Data
Description: Computes log-transformed kernel density estimates for positive data using a variety of kernels. It follows the methods
described in Jones, Nguyen and McLachlan (2018) <arXiv:1804.08365>.
Author: Hien D. Nguyen, Andrew T. Jones, and Geoffrey J. McLachlan
Maintainer: Andrew Thomas Jones <andrewthomasjones@gmail.com>
Diff between logKDE versions 0.3.0 dated 2018-07-23 and 0.3.1 dated 2018-07-24
DESCRIPTION | 8 - MD5 | 21 +- NEWS.md | 6 R/logKDE.R | 6 README.md | 300 +++++++++++++++++++++++++++++++++++--- inst/doc/logKDE.pdf |binary man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example1-1.png |only man/figures/README-example1-2.png |only man/figures/README-example2-1.png |only man/figures/README-example3-1.png |only man/figures/README-example4-1.png |only src/logKDE.cpp | 2 14 files changed, 305 insertions(+), 38 deletions(-)
Title: Connect to the 'jamovi' Statistical Spreadsheet
Description: Methods to access data sets from the 'jamovi' statistical
spreadsheet (see <https://www.jamovi.org> for more information) from R.
Author: Jonathon Love [aut, cre]
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvconnect versions 1.0.1 dated 2018-07-22 and 1.0.2 dated 2018-07-24
DESCRIPTION | 12 ++++---- MD5 | 8 ++--- R/eval.R | 28 ++++++++++++++++++-- R/main.R | 13 +++++++-- src/readdf.cpp | 78 ++++++++++++++++++++++++++++----------------------------- 5 files changed, 84 insertions(+), 55 deletions(-)
Title: Code Calibration in a Bayesian Framework
Description: Calibration of every computational code. It uses a Bayesian framework to rule the estimation. With a new data set, the prediction will create a prevision set taking into account the new calibrated parameters. The choices between several models is also available. The methods are described in the paper Carmassi et al. (2018) <arXiv:1801.01810>.
Author: Mathieu Carmassi [aut, cre]
Maintainer: Mathieu Carmassi <mathieu.carmassi@gmail.com>
Diff between CaliCo versions 0.1.0 dated 2018-03-15 and 0.1.1 dated 2018-07-24
CaliCo-0.1.0/CaliCo/R/prediction.R |only CaliCo-0.1.0/CaliCo/man/prediction.Rd |only CaliCo-0.1.0/CaliCo/man/prediction.class.Rd |only CaliCo-0.1.0/CaliCo/tests |only CaliCo-0.1.1/CaliCo/DESCRIPTION | 14 CaliCo-0.1.1/CaliCo/MD5 | 72 CaliCo-0.1.1/CaliCo/NAMESPACE | 13 CaliCo-0.1.1/CaliCo/R/CaliCo-package.R | 15 CaliCo-0.1.1/CaliCo/R/Kernel.R | 120 CaliCo-0.1.1/CaliCo/R/RcppExports.R | 28 CaliCo-0.1.1/CaliCo/R/calibration.R | 350 CaliCo-0.1.1/CaliCo/R/forecast.R |only CaliCo-0.1.1/CaliCo/R/functions.R | 502 CaliCo-0.1.1/CaliCo/R/models.R | 1248 CaliCo-0.1.1/CaliCo/R/prior.R | 177 CaliCo-0.1.1/CaliCo/R/sequentialDesign.R |only CaliCo-0.1.1/CaliCo/build/vignette.rds |binary CaliCo-0.1.1/CaliCo/inst/doc/CaliCo-introduction.R | 197 CaliCo-0.1.1/CaliCo/inst/doc/CaliCo-introduction.Rmd | 333 CaliCo-0.1.1/CaliCo/inst/doc/CaliCo-introduction.html |121016 ------------------ CaliCo-0.1.1/CaliCo/man/CaliCo.Rd | 13 CaliCo-0.1.1/CaliCo/man/MetropolisHastingsCpp.Rd | 12 CaliCo-0.1.1/CaliCo/man/MetropolisHastingsCppD.Rd | 12 CaliCo-0.1.1/CaliCo/man/calibrate.Rd | 50 CaliCo-0.1.1/CaliCo/man/calibrate.class.Rd | 2 CaliCo-0.1.1/CaliCo/man/chain.Rd |only CaliCo-0.1.1/CaliCo/man/estimators.Rd |only CaliCo-0.1.1/CaliCo/man/forecast.Rd |only CaliCo-0.1.1/CaliCo/man/forecast.class.Rd |only CaliCo-0.1.1/CaliCo/man/grapes-less-than-grapes.Rd |only CaliCo-0.1.1/CaliCo/man/model.Rd | 116 CaliCo-0.1.1/CaliCo/man/model.class.Rd | 16 CaliCo-0.1.1/CaliCo/man/multivariate.Rd | 3 CaliCo-0.1.1/CaliCo/man/prior.Rd | 13 CaliCo-0.1.1/CaliCo/man/prior.class.Rd | 6 CaliCo-0.1.1/CaliCo/man/seqDesign.class.Rd |only CaliCo-0.1.1/CaliCo/man/sequentialDesign.Rd |only CaliCo-0.1.1/CaliCo/man/unscale.Rd | 2 CaliCo-0.1.1/CaliCo/man/unscale.matrix.diag.Rd | 4 CaliCo-0.1.1/CaliCo/src/MCMC.cpp | 138 CaliCo-0.1.1/CaliCo/src/RcppExports.cpp | 16 CaliCo-0.1.1/CaliCo/vignettes/CaliCo-introduction.Rmd | 333 42 files changed, 2601 insertions(+), 122220 deletions(-)
Title: Nearest Neighbor Observation Imputation and Evaluation Tools
Description: Performs nearest neighbor-based imputation using one or more alternative
approaches to processing multivariate data. These include methods based on canonical
correlation analysis, canonical correspondence analysis, and a multivariate adaptation
of the random forest classification and regression techniques of Leo Breiman and Adele
Cutler. Additional methods are also offered. The package includes functions for
comparing the results from running alternative techniques, detecting imputation targets
that are notably distant from reference observations, detecting and correcting
for bias, bootstrapping and building ensemble imputations, and mapping results.
Author: Nicholas L. Crookston, Andrew O. Finley, John Coulston (Sunil Arya and David Mount for ANN)
Maintainer: Nicholas L. Crookston <ncrookston.fs@gmail.com>
Diff between yaImpute versions 1.0-29 dated 2017-12-10 and 1.0-30 dated 2018-07-24
DESCRIPTION | 14 ++++----- MD5 | 30 ++++++++++---------- NEWS | 8 +++++ R/newtargets.R | 26 ++++++++++++++++- R/varSelection.R | 8 ++++- R/yai.R | 69 ++++++++++++++++++++++++++++++++++++---------- data/MoscowMtStJoe.RData |binary data/TallyLake.RData |binary man/yai.Rd | 16 ++++++++-- src/ANN.cpp | 6 ++-- src/kd_fix_rad_search.cpp | 10 +++--- src/kd_pr_search.cpp | 12 ++++---- src/kd_search.cpp | 13 ++++---- src/kd_util.cpp | 10 +++--- src/pr_queue.h | 10 +++--- src/pr_queue_k.h | 2 - 16 files changed, 161 insertions(+), 73 deletions(-)
Title: Analyzing Real-Time Quantitative PCR Data
Description: Calculates the amplification efficiency and curves from real-time
quantitative PCR (Polymerase Chain Reaction) data. Estimates the relative
expression from PCR data using the double delta CT and the standard curve
methods Livak & Schmittgen (2001) <doi:10.1006/meth.2001.1262>. Tests for
statistical significance using two-group tests and linear regression
Yuan et al. (2006) <doi: 10.1186/1471-2105-7-85>.
Author: Mahmoud Ahmed [aut, cre]
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
Diff between pcr versions 1.1.1 dated 2018-06-23 and 1.1.2 dated 2018-07-24
DESCRIPTION | 8 ++--- MD5 | 14 ++++---- NAMESPACE | 1 NEWS.md | 4 ++ R/testing_fun.R | 46 ++++++++++++----------------- README.md | 2 - inst/doc/qpcr_analysis.html | 18 +++++------ tests/testthat/test_testing_fun.R | 60 +++++++++++++------------------------- 8 files changed, 66 insertions(+), 87 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-09 0.10.1
2016-04-24 0.9.4
2015-02-03 0.9.3
2014-11-15 0.9.2
2014-10-09 0.9.1
Title: Comparison of Algorithms with Iterative Sample Size Estimation
Description: Functions for performing experimental comparisons of algorithms
using adequate sample sizes for power and accuracy.
Author: Felipe Campelo [aut, cre],
Fernanda Takahashi [aut]
Maintainer: Felipe Campelo <fcampelo@ufmg.br>
Diff between CAISEr versions 0.3.0 dated 2018-06-19 and 0.3.3 dated 2018-07-24
DESCRIPTION | 13 MD5 | 30 NAMESPACE | 1 NEWS.md | 19 R/calc_nreps2.R | 38 R/calc_se.R | 2 R/consolidate_partial_results.R |only R/run_experiment.R | 33 README.md | 3 build/vignette.rds |binary inst/doc/Adapting_Algorithm_for_CAISEr.R | 7 inst/doc/Adapting_Algorithm_for_CAISEr.Rmd | 7 inst/doc/Adapting_Algorithm_for_CAISEr.html | 2348 ---------------------------- man/calc_nreps2.Rd | 6 man/consolidate.partial.results.Rd |only man/run_experiment.Rd | 4 vignettes/Adapting_Algorithm_for_CAISEr.Rmd | 7 17 files changed, 111 insertions(+), 2407 deletions(-)
Title: Accelerated Failure Time Model with Generalized Estimating
Equations
Description: A collection of methods for both the rank-based estimates and least-square estimates
to the Accelerated Failure Time (AFT) model.
For rank-based estimation, it provides approaches that include the computationally
efficient Gehan's weight and the general's weight such as the logrank weight.
Details of the rank-based estimation can be found in
Chiou et al. (2014) <doi:10.1007/s11222-013-9388-2> and
Chiou et al. (2015) <doi:10.1002/sim.6415>.
For the least-square estimation, the estimating equation is solved with
generalized estimating equations (GEE).
Moreover, in multivariate cases, the dependence working correlation structure
can be specified in GEE's setting.
Details on the least-squares estimation can be found in
Chiou et al. (2014) <doi:10.1007/s10985-014-9292-x>.
Author: Sy Han Chiou [aut, cre],
Sangwook Kang [aut],
Jun Yan [aut]
Maintainer: Sy Han Chiou <schiou@utdallas.edu>
Diff between aftgee versions 1.1-2 dated 2018-05-28 and 1.1.3 dated 2018-07-24
aftgee-1.1-2/aftgee/src/registerDynamicSymbol.c |only aftgee-1.1.3/aftgee/ChangeLog | 11 aftgee-1.1.3/aftgee/DESCRIPTION | 54 +- aftgee-1.1.3/aftgee/MD5 | 27 - aftgee-1.1.3/aftgee/NAMESPACE | 79 ++- aftgee-1.1.3/aftgee/R/aftgee.R | 221 ++++++++--- aftgee-1.1.3/aftgee/R/aftgee_pkg.R |only aftgee-1.1.3/aftgee/R/aftsrr.R | 480 +++++++++--------------- aftgee-1.1.3/aftgee/R/summary.R | 29 - aftgee-1.1.3/aftgee/inst/CITATION | 2 aftgee-1.1.3/aftgee/man/aftgee-package.Rd | 120 ++---- aftgee-1.1.3/aftgee/man/aftgee.Rd | 254 +++++------- aftgee-1.1.3/aftgee/man/aftgee.control.Rd | 46 +- aftgee-1.1.3/aftgee/man/aftsrr.Rd | 233 +++++------ aftgee-1.1.3/aftgee/src/aftgee.c | 6 aftgee-1.1.3/aftgee/src/init.c |only 16 files changed, 804 insertions(+), 758 deletions(-)