Title: Dynamic Network Clustering
Description: Community detection for dynamic networks, i.e., networks measured repeatedly over a sequence of discrete time points, using a latent space approach.
Author: Daniel K. Sewell
Maintainer: Dan Sewell <daniel-sewell@uiowa.edu>
Diff between dnc versions 1.1 dated 2016-05-14 and 1.2 dated 2016-05-16
DESCRIPTION | 6 ++-- MD5 | 20 ++++++++-------- R/DNCRPackageRCode.R | 4 +-- src/RcppExports.cpp | 56 +++++++++++++++++++++++----------------------- src/cLogLikelihood.cpp | 6 ++-- src/cVBUpdate.cpp | 28 +++++++++++------------ src/cVBnoClust.cpp | 30 ++++++++++++------------ src/cposteriorNoOmega.cpp | 8 +++--- src/csimulateData.cpp | 6 ++-- src/drawMiss.cpp | 6 ++-- src/drawXZar.cpp | 10 ++++---- 11 files changed, 90 insertions(+), 90 deletions(-)
Title: Robust Estimation of the Generalized log Gamma Model
Description: Robust estimation of the generalized log gamma model is provided using Quantile Tau estimator, Weighted Likelihood estimator and Truncated Maximum Likelihood estimator. Functions for regression and censored data are also available.
Author: Claudio Agostinelli <claudio.agostinelli@unitn.it>, Alfio Marazzi <Alfio.Marazzi@chuv.ch>, Victor Yohai <vyohai@uolsinectis.com.ar> and Alex Randriamiharisoa <Alex.Randriamiharisoa@chuv.ch>
Maintainer: Claudio Agostinelli <claudio.agostinelli@unitn.it>
Diff between robustloggamma versions 1.0-1 dated 2016-05-12 and 1.0-2 dated 2016-05-16
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/loggammacenslmrob.S.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
More information about robustloggamma at CRAN
Permanent link
Title: Random Forests for Survival, Regression and Classification
(RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes. Now extended to include multivariate and unsupervised forests.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.1.0 dated 2016-03-17 and 2.2.0 dated 2016-05-16
DESCRIPTION | 8 MD5 | 94 R/data.utilities.R | 23 R/factor.utilities.R | 2 R/find.interaction.R | 4 R/generic.impute.rfsrc.R | 6 R/generic.predict.rfsrc.R | 95 R/impute.rfsrc.R | 7 R/max.subtree.R | 2 R/plot.competing.risk.R | 2 R/plot.rfsrc.R | 10 R/plot.survival.R | 2 R/plot.variable.R | 2 R/predict.rfsrc.R | 4 R/print.rfsrc.R | 2 R/rf2rfz.R | 2 R/rfsrc.R | 174 + R/rfsrc.news.R | 2 R/rfsrcSyn.R | 90 R/stat.split.R | 2 R/utilities.R | 120 - R/var.select.R | 4 R/vimp.R | 2 R/zzz.R | 2 configure.ac | 2 data/breast.rda |binary data/follic.rda |binary data/hd.rda |binary data/nutrigenomic.rda |binary data/pbc.rda |binary data/vdv.rda |binary data/veteran.rda |binary data/wihs.rda |binary inst/NEWS | 19 inst/doc/rsf-Rnews.pdf |binary man/breast.Rd | 1 man/find.interaction.Rd | 5 man/impute.rfsrc.Rd | 24 man/plot.rfsrc.Rd | 30 man/predict.rfsrc.Rd | 14 man/rfsrc.Rd | 74 man/rfsrcSyn.Rd | 4 man/var.select.Rd | 13 man/vimp.Rd | 3 src/randomForestSRC.c | 4510 ++++++++++++++++++++++++---------------------- src/randomForestSRC.h | 371 ++- src/splitCustom.c | 16 src/splitCustom.h | 12 48 files changed, 3193 insertions(+), 2566 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an
abstraction for a value that may be available at some point in the future.
The state of a future can either be unresolved or resolved. As soon as it is
resolved, the value is available. Futures are useful constructs in for instance
concurrent evaluation, e.g. parallel processing and distributed processing on
compute clusters. The purpose of this package is to provide a lightweight
interface for using futures in R. Functions 'future()' and 'value()' exist for
creating futures and requesting their values, e.g.
'f <- future({ mandelbrot(c(0.28,0), side=2) })' and 'v <- value(f)'.
The 'resolved()' function can be used to check if a future is resolved or not.
An infix assignment operator '%<-%' exists for creating futures whose values
are accessible by the assigned variables (as promises), e.g.
'v %<-% { mandelbrot(c(0.28,0), side=2) }'.
This package implements synchronous "lazy" and "eager" futures, and asynchronous
"multicore", "multisession" and ad hoc "cluster" futures.
Globals variables and functions are automatically identified and exported.
Required packages are attached in external R sessions whenever needed.
All types of futures are designed to behave the same such that the exact
same code work regardless of futures used or number of cores, background
sessions or cluster nodes available.
Additional types of futures are provided by other packages enhancing
this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.13.0 dated 2016-04-14 and 0.14.0 dated 2016-05-16
DESCRIPTION | 10 MD5 | 87 +-- NAMESPACE | 11 NEWS | 13 R/ClusterFuture-class.R | 72 +- R/Future-class.R | 80 ++- R/FutureError-class.R |only R/LazyFuture-class.R | 2 R/MulticoreFuture-class.R | 4 R/MultiprocessFuture-class.R | 2 R/MultisessionFuture-class.R | 4 R/UniprocessFuture-class.R | 4 R/cluster.R | 13 R/multicore.R | 23 R/multiprocess.R | 6 R/multisession.R | 45 + R/nbrOfWorkers.R |only R/resolve.R | 23 R/signalEarly.R | 6 R/tweak.R | 12 R/values.R | 8 build/vignette.rds |binary inst/doc/future-1-overview.html | 165 +++--- inst/doc/future-3-topologies.html | 12 inst/doc/future-3-topologies.md.rsp | 12 inst/vignettes-static/incl/future-1-overview-example2.R | 40 - inst/vignettes-static/incl/future-1-overview-example3.R | 38 - man/ClusterFuture-class.Rd | 88 +-- man/Future-class.Rd | 97 ++- man/FutureError.Rd |only man/backtrace.Rd | 44 - man/cluster.Rd | 166 +++--- man/multicore.Rd | 200 ++++---- man/multiprocess.Rd | 152 +++--- man/multisession.Rd | 212 ++++---- man/nbrOfWorkers.Rd |only man/requestCore.Rd | 67 +- man/values.Rd | 50 +- tests/cluster.R | 8 tests/globals,resolve.R | 2 tests/invalid-owner.R | 8 tests/multicore.R | 6 tests/multiprocess.R | 14 tests/multisession.R | 14 tests/nbrOfWorkers.R |only tests/resolve.R | 400 ++++++++-------- vignettes/future-3-topologies.md.rsp | 12 47 files changed, 1196 insertions(+), 1036 deletions(-)
Title: Download, Clean and Generate New Variables from GSOD Data
Description: Download, clean and reformat weather data from USA National
Climatic Data Center (NCDC) Global Surface Summary of the Day (GSOD) weather
stations,
<https://data.noaa.gov/dataset/global-surface-summary-of-the-day-gsod>.
The function, get_GSOD(), retrieves data from the GSOD ftp site and
reformats it from United States Customary System (USCS) units to metric
units, also for convenience elevation is converted from decimetres to
metres. Stations are individually checked for number of missing days, as
defined by the user, to assure data quality. Stations with too many missing
observations are omitted from final file. Also omitted are stations with a
latitude of < -90 or > 90 or longitude of < - 180 or > 180. Output is
returned as a comma-separated values (CSV) file written to disk in a
location selected by the user, which summarises each year by station and
includes new variables: actual and saturation vapor pressure and relative
humidity calculated from the original GSOD data. The resulting files can be
as large as 500mb depending on the user's stringency for missing data and
geographic area of interest. Be sure to have sufficient RAM and disk space
as well as a reasonably fast internet connection to use this package to
perform this operation. However, for much smaller and more manageable data
sets, an individual country of interest may be selected as well as only
stations falling between -60/60 degrees latitude for agroclimatology work.
The resulting files include station data (e.g., station name, country,
latitude, longitude, elevation) for use in a geographic information system
(GIS). The function was largely based on T. Hengl's 'getGSOD.R' script,
available from
<http://spatial-analyst.net/book/system/files/getGSOD.R> with enhancements
to be more cross-platform, faster and more flexible. Currently flags are
maintained for all of the columns except for MIN/MAX. In the original
MIN/MAX columns of the GSOD data, "blank indicates max temp was taken from
the explicit max temp report and not from the 'hourly' data. * indicates max
temp was derived from the hourly data (i.e., highest hourly or
synoptic-reported temperature).", GSOD readme.txt
<http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>. For CSV files
resulting from GSODR the flags are stripped.
Author: Adam Sparks [aut, cre],
Tomislav Hengl [ctb],
Andy Nelson [ctb],
Kay Sumfleth [ctb]
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between GSODR versions 0.1.4 dated 2016-05-09 and 0.1.5 dated 2016-05-16
DESCRIPTION | 6 +- MD5 | 10 ++-- NEWS.md | 10 ++++ R/get_GSOD.R | 117 +++++++++++++++++++++++++++++++------------------------- README.md | 2 man/get_GSOD.Rd | 79 +++++++++++++++++++------------------ 6 files changed, 126 insertions(+), 98 deletions(-)
Title: Color Calculations with Emphasis on Spectral Data
Description: Calculate with spectral properties of light sources, materials, cameras, eyes, and scanners.
Build complex systems from simpler parts using a spectral product algebra. For light sources,
compute CCT and CRI. For object colors, compute optimal colors and Logvinenko coordinates.
Work with the standard CIE illuminants and color matching functions, and read spectra from
text files, including CGATS files. Sample text files, and 4 vignettes are included.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between colorSpec versions 0.5-2 dated 2016-05-15 and 0.5-3 dated 2016-05-16
ChangeLog | 8 ++++++- DESCRIPTION | 8 +++---- MD5 | 24 +++++++++++------------ inst/doc/blueflame.R | 2 - inst/doc/blueflame.pdf |binary inst/doc/blueflame.rnw | 5 ++-- inst/doc/gallery.pdf |binary inst/doc/lens-aging.pdf |binary inst/doc/optimals.pdf |binary inst/extdata/targets/CC_Avg30_spectrum_CGATS.txt | 3 -- man/chop.Rd | 2 - man/product.Rd | 2 - vignettes/blueflame.rnw | 5 ++-- 13 files changed, 33 insertions(+), 26 deletions(-)
Title: Miscellaneous Functions for Survival Data
Description: A collection of functions to help in the analysis of
right-censored survival data. These extend the methods available in
package:survival.
Author: Chris Dardis
Maintainer: Chris Dardis <christopherdardis@gmail.com>
Diff between survMisc versions 0.5.0 dated 2016-02-24 and 0.5.2 dated 2016-05-16
DESCRIPTION | 12 ++++++------ MD5 | 29 ++++++++++++++++------------- NAMESPACE | 6 ++++++ R/auto |only R/comp.R | 9 ++++++--- R/profLik.R |only R/rsq.R | 2 +- R/survMisc_package.R | 6 +++--- build/vignette.rds |binary inst/NEWS.Rd | 22 ++++++++++++++++++---- inst/doc/plots.R | 22 +++++++++++++++------- inst/doc/plots.Rnw | 30 +++++++++++++++++++++--------- inst/doc/plots.pdf |binary man/comp.Rd | 7 +++++-- man/profLik.Rd |only man/rsq.Rd | 2 +- vignettes/plots.Rnw | 30 +++++++++++++++++++++--------- 17 files changed, 119 insertions(+), 58 deletions(-)
Title: Test of Periodicity using Response Surface Regression
Description: Tests periodicity in short time series using response surface regression.
Author: M. S. Islam
Maintainer: M. S. Islam <shahed-sta@sust.edu>
Diff between pRSR versions 3.0.2 dated 2014-07-10 and 3.1.1 dated 2016-05-16
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 4 +--- man/FitHReg.Rd | 1 - man/GetFitHReg.Rd | 2 -- man/SimulateAR1.Rd | 1 - man/SimulateHReg.Rd | 2 -- man/pRSR-package.Rd | 9 +++++---- 8 files changed, 19 insertions(+), 26 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), productivity evaluation using distance measures: DDF (directional distance function), DEA (data envelopment analysis), SBM (slack-based measure), and SF (shortage function), benchmarking, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 2.1 dated 2016-03-24 and 2.2 dated 2016-05-16
DESCRIPTION | 8 - MD5 | 12 +- NAMESPACE | 3 NEWS | 11 ++ R/DJL-internal.R | 250 +++++++++++++++++++++++++------------------------- R/dm.mahalanobis.R |only R/target.spec.dea.R | 4 man/dm.mahalanobis.Rd |only 8 files changed, 152 insertions(+), 136 deletions(-)
Title: Binomial and Multinomial Additive Hazards Models
Description: Functions to fit the binomial and multinomial additive hazards models and to calculate the contribution of diseases/conditions to the disability prevalence, as proposed by Nusselder and Looman (2004) <DOI:10.1353/dem.2004.0017>.
Author: Renata T C Yokota, Caspar W N Looman, Wilma J Nusselder,
Herman Van Oyen, Geert Molenberghs
Maintainer: Renata T C Yokota <Renata.Yokota@wiv-isp.be>
Diff between addhaz versions 0.3 dated 2016-02-25 and 0.4 dated 2016-05-16
DESCRIPTION | 8 MD5 | 4 R/MultAddHaz.R | 998 +++++++++++++++++++++++++++------------------------------ 3 files changed, 492 insertions(+), 518 deletions(-)
Title: Access to Abbyy Optical Character Recognition (OCR) API
Description: Get text from images of text using Abbyy Cloud Optical Character
Recognition (OCR) API. Easily OCR images, barcodes, forms, documents with
machine readable zones, e.g. passports. Get the results in a variety of formats
including plain text and XML. To learn more about the Abbyy OCR API, see http://
ocrsdk.com/.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between abbyyR versions 0.3 dated 2016-02-04 and 0.4.0 dated 2016-05-16
abbyyR-0.3/abbyyR/NEWS |only abbyyR-0.3/abbyyR/R/compareText.R |only abbyyR-0.3/abbyyR/man/compareText.Rd |only abbyyR-0.4.0/abbyyR/DESCRIPTION | 10 abbyyR-0.4.0/abbyyR/MD5 | 85 ++- abbyyR-0.4.0/abbyyR/NAMESPACE | 4 abbyyR-0.4.0/abbyyR/NEWS.md |only abbyyR-0.4.0/abbyyR/R/abbyyR.R | 3 abbyyR-0.4.0/abbyyR/R/deleteTask.R | 4 abbyyR-0.4.0/abbyyR/R/getAppInfo.R | 20 abbyyR-0.4.0/abbyyR/R/getResults.R | 14 abbyyR-0.4.0/abbyyR/R/listFinishedTasks.R | 17 abbyyR-0.4.0/abbyyR/R/listTasks.R | 33 + abbyyR-0.4.0/abbyyR/R/processBarcodeField.R | 10 abbyyR-0.4.0/abbyyR/R/processBusinessCard.R | 6 abbyyR-0.4.0/abbyyR/R/processCheckmarkField.R | 9 abbyyR-0.4.0/abbyyR/R/processDocument.R | 13 abbyyR-0.4.0/abbyyR/R/processFields.R | 3 abbyyR-0.4.0/abbyyR/R/submitImage.R | 3 abbyyR-0.4.0/abbyyR/README.md | 2 abbyyR-0.4.0/abbyyR/build/vignette.rds |binary abbyyR-0.4.0/abbyyR/inst/doc/example.Rmd | 1 abbyyR-0.4.0/abbyyR/inst/doc/example.html | 169 +++++-- abbyyR-0.4.0/abbyyR/inst/doc/overview.Rmd | 1 abbyyR-0.4.0/abbyyR/inst/doc/overview.html | 165 +++++-- abbyyR-0.4.0/abbyyR/inst/doc/wiscads.Rmd | 1 abbyyR-0.4.0/abbyyR/inst/doc/wiscads.html | 219 ++++++---- abbyyR-0.4.0/abbyyR/man/getAppInfo.Rd | 8 abbyyR-0.4.0/abbyyR/man/getResults.Rd | 2 abbyyR-0.4.0/abbyyR/man/listFinishedTasks.Rd | 9 abbyyR-0.4.0/abbyyR/man/listTasks.Rd | 12 abbyyR-0.4.0/abbyyR/man/processBarcodeField.Rd | 2 abbyyR-0.4.0/abbyyR/man/processBusinessCard.Rd | 2 abbyyR-0.4.0/abbyyR/man/processCheckmarkField.Rd | 6 abbyyR-0.4.0/abbyyR/man/processDocument.Rd | 3 abbyyR-0.4.0/abbyyR/tests/testthat/abbyy_key |only abbyyR-0.4.0/abbyyR/tests/testthat/abbyy_key.enc |only abbyyR-0.4.0/abbyyR/tests/testthat/test-get-info.R | 12 abbyyR-0.4.0/abbyyR/tests/testthat/test-get-results.R | 14 abbyyR-0.4.0/abbyyR/tests/testthat/test-list-finished-tasks.R | 9 abbyyR-0.4.0/abbyyR/tests/testthat/test-list-tasks.R | 10 abbyyR-0.4.0/abbyyR/tests/testthat/test-submit-image.R | 9 abbyyR-0.4.0/abbyyR/vignettes/example.Rmd | 1 abbyyR-0.4.0/abbyyR/vignettes/example.md |only abbyyR-0.4.0/abbyyR/vignettes/overview.Rmd | 1 abbyyR-0.4.0/abbyyR/vignettes/overview.md |only abbyyR-0.4.0/abbyyR/vignettes/wiscads.Rmd | 1 abbyyR-0.4.0/abbyyR/vignettes/wiscads.md |only 48 files changed, 607 insertions(+), 286 deletions(-)
Title: Toolkit for Item Factor Analysis with OpenMx
Description: Tools, tutorials, and demos of Item Factor Analysis using OpenMx.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between ifaTools versions 0.8 dated 2015-10-17 and 0.10 dated 2016-05-16
DESCRIPTION | 12 +++++---- MD5 | 54 +++++++++++++++++++++++++++++++------------ NAMESPACE | 2 - build |only inst/doc |only inst/example/quadrature.R | 11 +++++--- inst/modelBuilder/server.R | 16 +++++++----- man/SitemPlot.Rd | 2 - man/addExploratoryFactors.Rd | 2 - man/iccPlot.Rd | 2 - man/itemModelExplorer.Rd | 2 - man/itemResponseMap.Rd | 2 - man/modelBuilder.Rd | 2 - man/plotInformation.Rd | 2 - man/replicateModelBy.Rd | 2 - man/uniquenessPrior.Rd | 2 - man/univariatePrior.Rd | 2 - vignettes |only 18 files changed, 75 insertions(+), 40 deletions(-)
Title: Integration of Functions Over Simplices
Description: Provides methods to integrate functions over m-dimensional simplices
in n-dimensional Euclidean space. There are exact methods for polynomials and
adaptive methods for integrating an arbitrary function. Dirichlet probabilities
are calculated in certain cases.
Author: John P. Nolan, with parts adapted from Fortran and matlab code by Alan Genz
Maintainer: John P. Nolan <jpnolan@american.edu>
Diff between SimplicialCubature versions 1.1 dated 2016-01-05 and 1.2 dated 2016-05-16
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 2 +- R/adsimp.R | 2 +- man/SimplicialCubature-package.Rd | 11 ++--------- man/integrateSimplexPolynomial.Rd | 2 +- 6 files changed, 15 insertions(+), 22 deletions(-)
More information about SimplicialCubature at CRAN
Permanent link
Title: Multivariate Meshes and Histograms in Arbitrary Dimensions
Description: Define, manipulate and plot meshes on simplices, spheres, balls, rectangles and tubes.
Directional and other multivariate histograms are provided.
Author: John P. Nolan
Maintainer: John P. Nolan <jpnolan@american.edu>
Diff between mvmesh versions 1.2 dated 2016-01-06 and 1.3 dated 2016-05-16
mvmesh-1.2/mvmesh/man/RectangularMesh.Rd |only mvmesh-1.3/mvmesh/DESCRIPTION | 8 - mvmesh-1.3/mvmesh/MD5 | 25 +-- mvmesh-1.3/mvmesh/NAMESPACE | 4 mvmesh-1.3/mvmesh/R/mvhist.R | 4 mvmesh-1.3/mvmesh/R/mvmesh.R | 227 +++++++++++++++++++++---------- mvmesh-1.3/mvmesh/demo/mvmesh.R | 20 +- mvmesh-1.3/mvmesh/demo/mvmesh2.R | 11 - mvmesh-1.3/mvmesh/demo/mvmeshmisc.R | 12 - mvmesh-1.3/mvmesh/man/HollowRectangle.Rd |only mvmesh-1.3/mvmesh/man/PolarSphere.Rd | 2 mvmesh-1.3/mvmesh/man/mvhist.Rd | 4 mvmesh-1.3/mvmesh/man/mvmesh-package.Rd | 22 --- mvmesh-1.3/mvmesh/man/mvmeshmisc.Rd | 14 - mvmesh-1.3/mvmesh/man/rmvmesh.Rd |only 15 files changed, 224 insertions(+), 129 deletions(-)
Title: Koul's Minimum Distance Estimation in Linear Regression and
Autoregression Model
Description: Consider linear regression model and autoregressive model of order q where errors in the linear regression model and innovations in the autoregression model are independent and symmetrically distributed. Hira L. Koul proposed a nonparametric minimum distance estimation method by minimizing L2-type distance between certain weighted residual empirical distribution functions. He also proposed a simpler version of the loss function by using symmetry of the integrating measure in the distance. This package contains three functions: KoulLrMde(), KoulArMde(), and Koul2StageMde(). KoulLrMde() and KoulArMde() provide minimum distance estimators for linear regression model and autoregression model, respectively, where both are based on Koul's method. These two functions take much less time for the computation than those based on parametric minimum distance estimation methods. Koul2StageMde() provides estimators for regression and autoregressive coefficients of linear regression model with autoregressive errors through minimum distant method of two stages.
Author: Jiwoong Kim [aut, cre]
Maintainer: Jiwoong Kim <kimjiwo2@stt.msu.edu>
Diff between KoulMde versions 2.0 dated 2016-05-12 and 2.0.1 dated 2016-05-16
KoulMde-2.0.1/KoulMde/DESCRIPTION | 8 KoulMde-2.0.1/KoulMde/MD5 | 12 KoulMde-2.0.1/KoulMde/NAMESPACE | 2 KoulMde-2.0.1/KoulMde/R/MdeFunc.R | 359 ++++++++++++++--------------- KoulMde-2.0.1/KoulMde/man/Koul2StageMde.Rd |only KoulMde-2.0.1/KoulMde/man/KoulArMde.Rd | 39 ++- KoulMde-2.0.1/KoulMde/man/KoulLrMde.Rd | 43 ++- KoulMde-2.0/KoulMde/man/Koul2StageMDE.Rd |only 8 files changed, 250 insertions(+), 213 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii)
Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v)
Matrix functions, (vi) Projector and canonical efficiency functions, and (vii)
Miscellaneous functions. A document 'daeDesignRandomization.pdf', available
in the doc subdirectory of the installation directory for 'dae', describes the
use of the package for generating randomized layouts for experiments. The ANOVA
functions facilitate the extraction of information when the 'Error' function has
been used in the call to 'aov'.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between dae versions 2.7-15 dated 2016-05-14 and 2.7-16 dated 2016-05-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/fac.gen.r | 5 ++++- build/partial.rdb |binary inst/NEWS.Rd | 5 +++++ inst/doc/dae-manual.pdf |binary 6 files changed, 18 insertions(+), 10 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 7-th 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 0.1-72 dated 2016-04-23 and 0.1-73 dated 2016-05-16
DESCRIPTION | 8 +++---- MD5 | 15 +++++++------- NAMESPACE | 5 ++-- R/FixedDiscrDiscrIT.R | 43 ++++++++++++++++++++++++------------------ R/ICA.BinCont.R | 2 - R/plot_ICABinCont.R | 10 ++++----- R/summary.FixedDIscrDiscrIT.R |only man/plot.ICABinCont.Rd | 2 - man/summary.gen.Rd | 2 + 9 files changed, 49 insertions(+), 38 deletions(-)
Title: Amazing Random Facts About the World's Greatest Hacker
Description: Display a randomly selected quote about Richard M. Stallman
based on the collection in the 'GNU Octave' function 'fact()' which was
aggregated by Jordi Gutiérrez Hermoso based on the (now defunct) site
<http://www.stallmanfacts.com>.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between rmsfact versions 0.0.1 dated 2016-05-15 and 0.0.2 dated 2016-05-16
ChangeLog | 13 ++++++++++++- DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- R/rmsfact.R | 1 + README.md | 24 ++++++++++++++++++++++-- inst/NEWS.Rd |only inst/rmsfact/rmsfact.txt | 24 ++++++++++++------------ 7 files changed, 57 insertions(+), 24 deletions(-)
Title: The CDK Libraries Packaged for R
Description: An R interface to the Chemistry Development Kit, a Java library
for chemoinformatics. Given the size of the library itself, this package is
not expected to change very frequently. To make use of the CDK within R, it is
suggested that you use the rcdk package. Note that it is possible to directly
interact with the CDK using rJava. However rcdk exposes functionality in a more
idiomatic way. The CDK library itself is released as LGPL and the sources can be
obtained from https://github.com/cdk/cdk.
Author: Rajarshi Guha [aut],
Zachary Charlop-Powers [cre],
CDK Project [ctb, cph] (CDK Java library contained in multiple jar
files)
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between rcdklibs versions 1.5.8.4 dated 2014-08-31 and 1.5.13 dated 2016-05-16
rcdklibs-1.5.13/rcdklibs/DESCRIPTION | 39 ++-- rcdklibs-1.5.13/rcdklibs/MD5 | 85 ---------- rcdklibs-1.5.13/rcdklibs/NEWS | 1 rcdklibs-1.5.13/rcdklibs/inst/cont/cdk-1.5.13.jar |only rcdklibs-1.5.13/rcdklibs/java/README | 4 rcdklibs-1.5.8.4/rcdklibs/inst/cont/Jama-1.0.2.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/asm-commons-3.3.1.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/beam-core-0.5.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/beam-func-0.5.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-annotation-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-atomtype-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-builder3d-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-builder3dtools-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-charges-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-cip-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-control-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-core-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-data-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-datadebug-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-dict-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-diff-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-extra-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-fingerprint-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-forcefield-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-formula-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-fragment-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-group-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-hash-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-interfaces-1.5.8-SNAPSHOT.jar |only 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rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-qsaratomic-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-qsarbond-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-qsarcml-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-qsarionpot-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-qsarmolecular-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-qsarprotein-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-reaction-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-render-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-renderawt-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-renderbasic-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-renderextra-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-sdg-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-signature-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-silent-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-smarts-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-smiles-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-smsd-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-standard-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-structgen-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-tautomer-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cdk-valencycheck-1.5.8-SNAPSHOT.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/cmlxom-3.1.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/commons-beanutils-1.7.0.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/commons-io-2.0.1.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/commons-math-2.2.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/commons-math3-3.1.1.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/euclid-1.0.1.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/guava-14.0.1.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/jgrapht-0.6.0.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/joda-time-1.6.2.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/log4j-1.2.17.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/signatures-1.1.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/slf4j-api-1.6.4.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/tagsoup-1.2.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/vecmath-1.5.2.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/xalan-2.7.0.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/xercesImpl-2.8.0.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/xml-apis-1.3.03.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/xom-1.2.5.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/xpp3-1.1.4c.jar |only rcdklibs-1.5.8.4/rcdklibs/inst/cont/xpp3_min-1.1.4c.jar |only 83 files changed, 28 insertions(+), 101 deletions(-)
Title: Interface to the CDK Libraries
Description: Allows the user to access functionality in the
CDK, a Java framework for cheminformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors and so on.
In addition the CDK API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph],
Zachary Charlop-Powers [cre]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between rcdk versions 3.3.2 dated 2014-10-13 and 3.3.5 dated 2016-05-16
DESCRIPTION | 29 ++++++++++++++++------------- MD5 | 37 +++++++++++++++++++------------------ NAMESPACE | 4 +++- NEWS | 2 ++ R/desc.R | 24 +++++++++++++++++++----- R/iterating.R | 2 -- R/smiles.R | 8 +++++++- R/visual.R | 21 ++++++++++++++++----- build/vignette.rds |binary inst/CITATION | 2 +- inst/cont/rcdk.jar |binary inst/doc/rcdk.R | 4 ++-- inst/doc/rcdk.Rnw | 4 ++-- inst/doc/rcdk.pdf |binary inst/unitTests/runit.depiction.R |only inst/unitTests/runit.props.R | 4 ++-- inst/unitTests/runit.rcdk.R | 2 +- man/evaldesc.Rd | 2 +- man/getsmiles.Rd | 3 +-- vignettes/rcdk.Rnw | 4 ++-- 20 files changed, 94 insertions(+), 58 deletions(-)
Title: A Fast, Flexible Tool for Sorting Phylogenetic Trees
Description: Screens and sorts phylogenetic trees in both traditional and
extended Newick format. Allows for the fast and flexible screening (within
a tree) of Exclusive clades that comprise only the target taxa and/or Non-
Exclusive clades that includes a defined portion of non-target taxa.
Author: Timothy Stephens [aut, cre, trl] (R port),
Debashish Bhattacharya [aut],
Mark Ragan [aut],
Cheong Xin Chan [aut, cph] (Original Perl implementation)
Maintainer: Timothy Stephens <timothy.stephens1@uqconnect.edu.au>
Diff between PhySortR versions 1.0.6 dated 2016-03-22 and 1.0.7 dated 2016-05-16
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/PhySortR.Rd | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Individual Tree Crowns Segmentation
Description: Two methods for Individual Tree Crowns (ITCs) delineation on remote sensing data: one is based on LiDAR data in x,y,z format and one on imagery data in raster format.
Author: Michele Dalponte
Maintainer: Michele Dalponte <michele.dalponte@fmach.it>
Diff between itcSegment versions 0.1 dated 2016-02-29 and 0.2 dated 2016-05-16
itcSegment-0.1/itcSegment/R/otsu.R |only itcSegment-0.2/itcSegment/DESCRIPTION | 10 ++-- itcSegment-0.2/itcSegment/MD5 | 13 ++--- itcSegment-0.2/itcSegment/R/itcIMG.R | 26 +++++++---- itcSegment-0.2/itcSegment/R/itcLiDAR.R | 67 +++++++++++++++++++++++++++-- itcSegment-0.2/itcSegment/data/imgData.rda |binary itcSegment-0.2/itcSegment/man/itcIMG.Rd | 16 ++++-- itcSegment-0.2/itcSegment/man/itcLiDAR.Rd | 8 +-- 8 files changed, 105 insertions(+), 35 deletions(-)
Title: Download and Process Public Domain Works from Project Gutenberg
Description: Download and process public domain works in the Project
Gutenberg collection. Includes metadata for all Project Gutenberg works,
so that they can be searched and retrieved.
Author: David Robinson [aut, cre]
Maintainer: David Robinson <admiral.david@gmail.com>
Diff between gutenbergr versions 0.1 dated 2016-05-03 and 0.1.1 dated 2016-05-16
gutenbergr-0.1.1/gutenbergr/DESCRIPTION | 14 gutenbergr-0.1.1/gutenbergr/MD5 | 52 - gutenbergr-0.1.1/gutenbergr/NEWS.md | 12 gutenbergr-0.1.1/gutenbergr/R/data.R | 55 + gutenbergr-0.1.1/gutenbergr/R/globals.R | 3 gutenbergr-0.1.1/gutenbergr/R/gutenberg_download.R | 53 + gutenbergr-0.1.1/gutenbergr/R/gutenberg_works.R | 76 +- gutenbergr-0.1.1/gutenbergr/R/utils.R | 10 gutenbergr-0.1.1/gutenbergr/README.md | 67 + gutenbergr-0.1.1/gutenbergr/build/vignette.rds |binary gutenbergr-0.1.1/gutenbergr/data/gutenberg_authors.rda |binary gutenbergr-0.1.1/gutenbergr/data/gutenberg_metadata.rda |binary gutenbergr-0.1.1/gutenbergr/data/gutenberg_subjects.rda |binary gutenbergr-0.1.1/gutenbergr/inst/doc/intro.R | 44 - gutenbergr-0.1.1/gutenbergr/inst/doc/intro.Rmd | 91 +- gutenbergr-0.1.1/gutenbergr/inst/doc/intro.html | 475 +++++-------- gutenbergr-0.1.1/gutenbergr/man/gutenberg_authors.Rd | 22 gutenbergr-0.1.1/gutenbergr/man/gutenberg_download.Rd | 17 gutenbergr-0.1.1/gutenbergr/man/gutenberg_get_mirror.Rd | 8 gutenbergr-0.1.1/gutenbergr/man/gutenberg_metadata.Rd | 21 gutenbergr-0.1.1/gutenbergr/man/gutenberg_strip.Rd | 15 gutenbergr-0.1.1/gutenbergr/man/gutenberg_subjects.Rd | 16 gutenbergr-0.1.1/gutenbergr/man/gutenberg_works.Rd | 46 - gutenbergr-0.1.1/gutenbergr/tests/testthat/test-download.R | 34 gutenbergr-0.1.1/gutenbergr/tests/testthat/test-metadata.R | 38 + gutenbergr-0.1.1/gutenbergr/tests/testthat/test-utils.R |only gutenbergr-0.1.1/gutenbergr/vignettes/intro.Rmd | 91 +- gutenbergr-0.1/gutenbergr/LICENSE |only 28 files changed, 782 insertions(+), 478 deletions(-)
Title: Genetic Algorithms
Description: An R package for optimisation using genetic algorithms. The package provides a flexible general-purpose set of tools for implementing genetic algorithms search in both the continuous and discrete case, whether constrained or not. Users can easily define their own objective function depending on the problem at hand. Several genetic operators are available and can be combined to explore the best settings for the current task. Furthermore, users can define new genetic operators and easily evaluate their performances. Local search using general-purpose optimisation algorithms can be applied stochastically to exploit interesting regions. GAs can be run sequentially or in parallel, using an explicit master-slave parallelisation or a coarse-grain islands approach.
Author: Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between GA versions 3.0 dated 2016-05-10 and 3.0.1 dated 2016-05-16
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/ga.R | 7 +++++-- R/gaIslands.R | 10 +++++----- README.md | 35 +++++++++++++++++++++++++++++++++-- inst/NEWS | 9 ++++++++- inst/doc/GA.html | 51 +++++++++++++++++++++++++-------------------------- man/ga.Rd | 2 +- man/gaisl.Rd | 3 +-- 10 files changed, 94 insertions(+), 55 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and
inference.
This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB,
MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing
and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms
for discrete, Gaussian and conditional Gaussian networks, along with many
score functions and conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are
also implemented.
Some utility functions (model comparison and manipulation, random data
generation, arc orientation testing, simple and advanced plots) are
included, as well as support for parameter estimation (maximum likelihood
and Bayesian) and inference, conditional probability queries and
cross-validation. Development snapshots with the latest bugfixes are
available from www.bnlearn.com.
Author: Marco Scutari
Maintainer: Marco Scutari <marco.scutari@gmail.com>
Diff between bnlearn versions 3.9 dated 2015-11-27 and 4.0 dated 2016-05-16
bnlearn-3.9/bnlearn/src/include/allocations.h |only bnlearn-4.0/bnlearn/Changelog | 45 ++ bnlearn-4.0/bnlearn/DESCRIPTION | 8 bnlearn-4.0/bnlearn/MD5 | 239 +++++++-------- bnlearn-4.0/bnlearn/NAMESPACE | 2 bnlearn-4.0/bnlearn/R/arc.operations.R | 22 + bnlearn-4.0/bnlearn/R/arc.strength.R | 33 +- bnlearn-4.0/bnlearn/R/backend-indep.R | 11 bnlearn-4.0/bnlearn/R/classifiers.R | 1 bnlearn-4.0/bnlearn/R/cpdag.R |only bnlearn-4.0/bnlearn/R/cv.R | 9 bnlearn-4.0/bnlearn/R/fitted.assignment.R | 2 bnlearn-4.0/bnlearn/R/frontend-amat.R | 30 + bnlearn-4.0/bnlearn/R/frontend-arcs.R | 51 ++- bnlearn-4.0/bnlearn/R/frontend-bn.R | 19 - bnlearn-4.0/bnlearn/R/frontend-bootstrap.R | 6 bnlearn-4.0/bnlearn/R/frontend-fit.R | 4 bnlearn-4.0/bnlearn/R/frontend-graph.R | 10 bnlearn-4.0/bnlearn/R/frontend-learning.R | 10 bnlearn-4.0/bnlearn/R/frontend-nodes.R | 12 bnlearn-4.0/bnlearn/R/frontend-plot.R | 4 bnlearn-4.0/bnlearn/R/frontend-predict.R | 26 + bnlearn-4.0/bnlearn/R/frontend-print.R | 13 bnlearn-4.0/bnlearn/R/frontend-score.R | 18 + bnlearn-4.0/bnlearn/R/frontend-strength.R | 52 +++ bnlearn-4.0/bnlearn/R/globals.R | 22 - bnlearn-4.0/bnlearn/R/hill-climbing.R | 4 bnlearn-4.0/bnlearn/R/hiton-pc.R | 10 bnlearn-4.0/bnlearn/R/init.R | 40 +- bnlearn-4.0/bnlearn/R/lattice.R | 4 bnlearn-4.0/bnlearn/R/learning-algorithms.R | 21 - bnlearn-4.0/bnlearn/R/loss.R | 12 bnlearn-4.0/bnlearn/R/maxmin-pc.R | 10 bnlearn-4.0/bnlearn/R/nparams.R | 3 bnlearn-4.0/bnlearn/R/predict.R | 8 bnlearn-4.0/bnlearn/R/scores.R | 9 bnlearn-4.0/bnlearn/R/tabu.R | 4 bnlearn-4.0/bnlearn/R/utils-graph.R | 67 ---- bnlearn-4.0/bnlearn/R/utils-misc.R | 31 + bnlearn-4.0/bnlearn/R/utils-sanitization.R | 49 ++- bnlearn-4.0/bnlearn/inst/bibtex/bnlearn.bib | 5 bnlearn-4.0/bnlearn/man/alpha.star.Rd |only bnlearn-4.0/bnlearn/man/arc.strength.Rd | 37 +- bnlearn-4.0/bnlearn/man/arcops.Rd | 12 bnlearn-4.0/bnlearn/man/bn.class.Rd | 3 bnlearn-4.0/bnlearn/man/bn.cv.Rd | 37 +- bnlearn-4.0/bnlearn/man/bn.fit.methods.Rd | 12 bnlearn-4.0/bnlearn/man/bn.strength-class.Rd | 4 bnlearn-4.0/bnlearn/man/bnlearn-package.Rd | 4 bnlearn-4.0/bnlearn/man/compare.Rd | 9 bnlearn-4.0/bnlearn/man/constraint.Rd | 37 ++ bnlearn-4.0/bnlearn/man/coronary.Rd | 2 bnlearn-4.0/bnlearn/man/cpdag.Rd | 9 bnlearn-4.0/bnlearn/man/foreign.Rd | 4 bnlearn-4.0/bnlearn/man/graph.Rd | 5 bnlearn-4.0/bnlearn/man/hc.Rd | 2 bnlearn-4.0/bnlearn/man/learn.Rd | 2 bnlearn-4.0/bnlearn/man/marks.Rd | 2 bnlearn-4.0/bnlearn/man/mb.Rd | 9 bnlearn-4.0/bnlearn/man/mmpc.Rd | 45 -- bnlearn-4.0/bnlearn/man/modelstring.Rd | 6 bnlearn-4.0/bnlearn/man/score.Rd | 46 +- bnlearn-4.0/bnlearn/src/acyclic.c | 139 ++++---- bnlearn-4.0/bnlearn/src/allocations.c | 80 +++-- bnlearn-4.0/bnlearn/src/allsubs.test.c | 131 ++++---- bnlearn-4.0/bnlearn/src/alpha.star.c |only bnlearn-4.0/bnlearn/src/arcs2amat.c | 26 - bnlearn-4.0/bnlearn/src/arcs2elist.c | 9 bnlearn-4.0/bnlearn/src/averaging.c | 181 +++++++++++ bnlearn-4.0/bnlearn/src/bayesian.network.c | 14 bnlearn-4.0/bnlearn/src/bind.c | 2 bnlearn-4.0/bnlearn/src/bn.recovery.c | 9 bnlearn-4.0/bnlearn/src/cache.structure.c | 31 - bnlearn-4.0/bnlearn/src/cextend.c |only bnlearn-4.0/bnlearn/src/cg.assumptions.c | 56 ++- bnlearn-4.0/bnlearn/src/cg.loglikelihood.c | 41 +- bnlearn-4.0/bnlearn/src/cg.mutual.information.c | 20 - bnlearn-4.0/bnlearn/src/common.c | 37 +- bnlearn-4.0/bnlearn/src/configurations.c | 12 bnlearn-4.0/bnlearn/src/contincency.tables.c | 27 + bnlearn-4.0/bnlearn/src/cpdag.c | 358 ++++++++--------------- bnlearn-4.0/bnlearn/src/ctest.c | 73 ++-- bnlearn-4.0/bnlearn/src/dedup.c | 15 bnlearn-4.0/bnlearn/src/dirichlet.posterior.c | 12 bnlearn-4.0/bnlearn/src/discrete.loglikelihood.c | 19 - bnlearn-4.0/bnlearn/src/discrete.monte.carlo.c | 35 +- bnlearn-4.0/bnlearn/src/discrete.tests.c | 10 bnlearn-4.0/bnlearn/src/filter.arcs.c | 2 bnlearn-4.0/bnlearn/src/fitted.c | 11 bnlearn-4.0/bnlearn/src/gaussian.loglikelihood.c | 5 bnlearn-4.0/bnlearn/src/gaussian.monte.carlo.c | 54 ++- bnlearn-4.0/bnlearn/src/graph.generation.c | 73 ++-- bnlearn-4.0/bnlearn/src/graph.priors.c | 32 +- bnlearn-4.0/bnlearn/src/hc.cache.lookup.c | 30 + bnlearn-4.0/bnlearn/src/htest.c | 2 bnlearn-4.0/bnlearn/src/include/blas.h | 1 bnlearn-4.0/bnlearn/src/include/bn.h | 7 bnlearn-4.0/bnlearn/src/include/graph.h | 6 bnlearn-4.0/bnlearn/src/include/loss.h | 3 bnlearn-4.0/bnlearn/src/include/rcore.h | 20 + bnlearn-4.0/bnlearn/src/include/tests.h | 1 bnlearn-4.0/bnlearn/src/is.dag.c | 7 bnlearn-4.0/bnlearn/src/jonckheere.c | 10 bnlearn-4.0/bnlearn/src/likelihood.weighting.c | 2 bnlearn-4.0/bnlearn/src/linear.algebra.c | 43 +- bnlearn-4.0/bnlearn/src/loss.c | 82 ++--- bnlearn-4.0/bnlearn/src/map.lw.c | 97 +++++- bnlearn-4.0/bnlearn/src/mi.matrix.c | 71 +++- bnlearn-4.0/bnlearn/src/nparams.c | 5 bnlearn-4.0/bnlearn/src/path.c | 45 +- bnlearn-4.0/bnlearn/src/pdag2dag.c | 11 bnlearn-4.0/bnlearn/src/per.node.score.c | 27 - bnlearn-4.0/bnlearn/src/predict.c | 181 ++++++++--- bnlearn-4.0/bnlearn/src/rbn.c | 55 +-- bnlearn-4.0/bnlearn/src/roundrobin.test.c | 105 ++++-- bnlearn-4.0/bnlearn/src/sanitization.c | 8 bnlearn-4.0/bnlearn/src/score.delta.c | 5 bnlearn-4.0/bnlearn/src/shrinkage.c | 70 +++- bnlearn-4.0/bnlearn/src/subsets.c | 4 bnlearn-4.0/bnlearn/src/tabu.c | 28 + bnlearn-4.0/bnlearn/src/tiers.c | 9 bnlearn-4.0/bnlearn/src/utest.c | 25 - bnlearn-4.0/bnlearn/src/wishart.posterior.c | 55 +-- 123 files changed, 2283 insertions(+), 1459 deletions(-)