Title: Fast Specialized CSV File Loader.
Diff between csvread versions 1.0 dated 2014-06-25 and 1.1 dated 2014-11-11
Description: This package provides functions for loading large (10M+ lines) CSV
and other delimited files, similar to read.csv, but typically faster and
using less memory than the standard R loader. While not entirely general,
it covers many common use cases when the types of columns in the CSV file
are known in advance. In addition, the package provides a class 'int64',
which represents 64-bit integers exactly when reading from a file. The
latter is useful when working with 64-bit integer identifiers exported from
databases. The CSV file loader supports common column types including
'integer', 'double', 'string', and 'int64', leaving further type
transformations to the user.
Author: Sergei Izrailev
Maintainer: Sergei Izrailev
DESCRIPTION | 8 ++++----
MD5 | 15 ++++++++-------
NAMESPACE | 1 +
NEWS | 7 ++++++-
R/longint.R | 10 ++++++++++
README.md | 2 ++
inst/csvread_1.1.pdf |only
man/int64.Rd | 3 +++
src/int64.h | 9 ++++++++-
9 files changed, 42 insertions(+), 13 deletions(-)
Title: Inference, aggregation and visualization for top-k ranked lists
Diff between TopKLists versions 1.0.2 dated 2014-06-25 and 1.0.3 dated 2014-11-11
Description: For multiple ranked input lists (full or partial) representing the same set of N objects, the package TopKLists offers (1) statistical inference on the lengths of informative top-k lists, (2) stochastic aggregation of full or partial lists, and (3) graphical tools for the statistical exploration of input lists, and for the visualization of aggregation results.
Author: Michael G. SchimekEva Budinska, Jie Ding, Karl G. Kugler, Vendula Svendova, Shili Lin
Maintainer: Michael G. Schimek
TopKLists-1.0.2/TopKLists/data/TopKGUISampleInput.rda |only
TopKLists-1.0.2/TopKLists/man/TopKGUISampleInput.Rd |only
TopKLists-1.0.3/TopKLists/DESCRIPTION | 19
TopKLists-1.0.3/TopKLists/MD5 | 41
TopKLists-1.0.3/TopKLists/NEWS | 7
TopKLists-1.0.3/TopKLists/R/TopKGraphics.R | 220 -
TopKLists-1.0.3/TopKLists/R/TopKInference.R | 5
TopKLists-1.0.3/TopKLists/build/vignette.rds |binary
TopKLists-1.0.3/TopKLists/data/TopKSpaceSampleInput.rda |binary
TopKLists-1.0.3/TopKLists/data/breast.rda |binary
TopKLists-1.0.3/TopKLists/data/datalist | 1
TopKLists-1.0.3/TopKLists/inst/doc/TopKLists.R | 86
TopKLists-1.0.3/TopKLists/inst/doc/TopKLists.Rnw | 1542 ++++++-------
TopKLists-1.0.3/TopKLists/inst/doc/TopKLists.pdf |binary
TopKLists-1.0.3/TopKLists/man/TopKListsGUI.Rd | 8
TopKLists-1.0.3/TopKLists/man/aggmap.Rd | 4
TopKLists-1.0.3/TopKLists/man/breast.Rd | 8
TopKLists-1.0.3/TopKLists/man/calculate.maxK.Rd | 6
TopKLists-1.0.3/TopKLists/man/compute.stream.Rd | 1
TopKLists-1.0.3/TopKLists/man/deltaplot.Rd | 6
TopKLists-1.0.3/TopKLists/src/TopK.c | 2
TopKLists-1.0.3/TopKLists/vignettes/TopKLists.Rnw | 1542 ++++++-------
TopKLists-1.0.3/TopKLists/vignettes/TopKLists_workflow.pdf |only
23 files changed, 1822 insertions(+), 1676 deletions(-)
Title: Framework for the analysis of genomic prediction data using R
Diff between synbreed versions 0.10-3 dated 2014-10-22 and 0.10-4 dated 2014-11-11
Description: The package 'synbreed' was developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). It contains a collection of functions required for genomic prediction in both plant and animal breeding. This covers data processing, data visualization and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
R/plot.relationshipMatrix.r | 39 +++++++++++++++++++++++++++++----------
R/summary.relationshipMatrix.r | 32 +++++++++++++++++++++++---------
4 files changed, 62 insertions(+), 29 deletions(-)
Title: Parameter estimation for the averaging model of Information
Integration Theory
Diff between rAverage versions 0.3-6 dated 2012-08-03 and 0.4-10 dated 2014-11-11
Description: Parameter estimation for averaging models of Anderson's Information Integration Theory
Author: Giulio Vidotto
Maintainer: Davide Massidda
rAverage-0.3-6/rAverage/man/averaging.Rd |only
rAverage-0.3-6/rAverage/man/rav.cmd.Rd |only
rAverage-0.3-6/rAverage/man/rav.indexes.Rd |only
rAverage-0.4-10/rAverage/DESCRIPTION | 23
rAverage-0.4-10/rAverage/MD5 | 43
rAverage-0.4-10/rAverage/NAMESPACE | 26
rAverage-0.4-10/rAverage/R/classes.methods.R | 335 +++---
rAverage-0.4-10/rAverage/R/fun.rav.R | 447 ++++++--
rAverage-0.4-10/rAverage/R/optim.rav.R | 82 +
rAverage-0.4-10/rAverage/R/rAverage.R | 66 +
rAverage-0.4-10/rAverage/R/rav.R | 678 ++++++++----
rAverage-0.4-10/rAverage/R/rav.cmd.R | 1242 -----------------------
rAverage-0.4-10/rAverage/data/pasta.rda |binary
rAverage-0.4-10/rAverage/man/datgen.Rd |only
rAverage-0.4-10/rAverage/man/fmdata1.Rd | 16
rAverage-0.4-10/rAverage/man/outlier.replace.Rd |only
rAverage-0.4-10/rAverage/man/pargen.Rd | 16
rAverage-0.4-10/rAverage/man/pasta.Rd | 17
rAverage-0.4-10/rAverage/man/rAverage-package.Rd | 48
rAverage-0.4-10/rAverage/man/rav.Rd | 292 +++--
rAverage-0.4-10/rAverage/man/rav.grid.Rd |only
rAverage-0.4-10/rAverage/man/rav.indices.Rd |only
rAverage-0.4-10/rAverage/man/rav.single.Rd |only
rAverage-0.4-10/rAverage/man/rav2file.Rd |only
rAverage-0.4-10/rAverage/src/averaging.c | 3
rAverage-0.4-10/rAverage/src/rAverage.h | 3
rAverage-0.4-10/rAverage/src/residual.c | 59 +
27 files changed, 1434 insertions(+), 1962 deletions(-)
Title: Design and analysis of mixture experiments
Diff between mixexp versions 1.1.2 dated 2014-05-28 and 1.1.8 dated 2014-11-11
Description: This package contains functions for creating designs for mixture experiments, making ternary contour plots, and making mixture effect plots.
Author: John Lawson
Maintainer: John Lawson
mixexp-1.1.2/mixexp/R/Effplot.R |only
mixexp-1.1.2/mixexp/man/Effplot.Rd |only
mixexp-1.1.8/mixexp/DESCRIPTION | 14
mixexp-1.1.8/mixexp/MD5 | 38 +-
mixexp-1.1.8/mixexp/NAMESPACE | 25 -
mixexp-1.1.8/mixexp/R/DesignPoints.R | 100 +++--
mixexp-1.1.8/mixexp/R/EffPlot.R |only
mixexp-1.1.8/mixexp/R/MixModel.R |only
mixexp-1.1.8/mixexp/R/MixturePlot.R | 505 +++++++++++++++---------------
mixexp-1.1.8/mixexp/R/ModelEff.R |only
mixexp-1.1.8/mixexp/R/Xvert.R | 172 ++++++----
mixexp-1.1.8/mixexp/R/cubic.R |only
mixexp-1.1.8/mixexp/data/Burn.rda |only
mixexp-1.1.8/mixexp/data/SneeMq.rda |binary
mixexp-1.1.8/mixexp/data/conmx.rda |binary
mixexp-1.1.8/mixexp/man/Burn.Rd |only
mixexp-1.1.8/mixexp/man/DesignPoints.Rd | 10
mixexp-1.1.8/mixexp/man/EffPlot.Rd |only
mixexp-1.1.8/mixexp/man/Fillv.Rd | 2
mixexp-1.1.8/mixexp/man/MixModel.Rd |only
mixexp-1.1.8/mixexp/man/MixturePlot.Rd | 12
mixexp-1.1.8/mixexp/man/ModelEff.Rd |only
mixexp-1.1.8/mixexp/man/ModelPlot.Rd | 7
mixexp-1.1.8/mixexp/man/Xvert.Rd | 44 +-
mixexp-1.1.8/mixexp/man/cubic.Rd |only
mixexp-1.1.8/mixexp/man/mixexp-package.Rd | 1
26 files changed, 494 insertions(+), 436 deletions(-)
Title: DepthProc
Diff between DepthProc versions 1.0.2 dated 2014-11-10 and 1.0.3 dated 2014-11-11
Description: Data depth concept offers a variety of powerful and user friendly tools for robust exploration and inference for multivariate data. The offered techniques may be successfully used in cases of lack of our knowledge on parametric models generating data due to their nonparametric nature. The package consist of among others implementations of several data depth techniques involving multivariate quantile-quantile plots, multivariate scatter estimators, multivariate Wilcoxon tests and robust regressions.
Author: Daniel Kosiorowski, Mateusz Bocian, Anna Wegrzynkiewicz and Zygmunt
Zawadzki from Cracow University of Economics.
Maintainer: Zygmunt Zawadzki
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
src/Depth.cpp | 25 ++++++++++++++-----------
3 files changed, 22 insertions(+), 19 deletions(-)
Title: Categorical Data
Diff between catdata versions 1.2 dated 2014-02-24 and 1.2.1 dated 2014-11-11
Description: This R-package contains examples from the book "Regression for Categorical Data", Tutz 2011, Cambridge University Press. The names of the examples refer to the chapter and the data set that is used.
Author: Gunther Schauberger, Gerhard Tutz
Maintainer: Gunther Schauberger
DESCRIPTION | 12
MD5 | 146 +++---
build/vignette.rds |binary
data/addiction.rda |binary
data/aids.rda |binary
data/birth.rda |binary
data/children.rda |binary
data/deathpenalty.rda |binary
data/dust.rda |binary
data/encephalitis.rda |binary
data/foodstamp.rda |binary
data/glass.rda |binary
data/heart.rda |binary
data/insolvency.rda |binary
data/knee.rda |binary
data/kneecumulative.rda |binary
data/kneesequential.rda |binary
data/leukoplakia.rda |binary
data/medcare.rda |binary
data/reader.rda |binary
data/recovery.rda |binary
data/rent.rda |binary
data/retinopathy.rda |binary
data/teratology.rda |binary
data/teratology2.rda |binary
data/unemployment.rda |binary
data/vaso.rda |binary
inst/doc/altbin-teratology.R | 280 ++++++------
inst/doc/binary-unemployment.R | 234 +++++-----
inst/doc/binary-vaso.R | 62 +-
inst/doc/count-children.R | 144 +++---
inst/doc/count-encephalitis.R | 80 +--
inst/doc/count-insolvency.R | 96 ++--
inst/doc/count-medcare.R | 158 +++----
inst/doc/loglinear-birth.R | 244 +++++-----
inst/doc/loglinear-leukoplakia.R | 76 +--
inst/doc/modbin-dust.R | 80 +--
inst/doc/modbin-foodstamp.R | 46 +-
inst/doc/modbin-unemployment1.R | 106 ++--
inst/doc/modbin-unemployment2.R | 260 +++++------
inst/doc/modbin-unemployment2.pdf |binary
inst/doc/multinomial-addiction1.R | 244 +++++-----
inst/doc/multinomial-addiction2.R | 104 ++--
inst/doc/multinomial-party1.R | 126 ++---
inst/doc/multinomial-party2.R | 164 +++----
inst/doc/multinomial-travel.R | 184 ++++----
inst/doc/multivariate-birth1.R | 122 ++---
inst/doc/multivariate-birth2.R | 244 +++++-----
inst/doc/multivariate-knee.R | 390 ++++++++---------
inst/doc/ordinal-arthritis.R | 84 +--
inst/doc/ordinal-knee1.R | 314 +++++++-------
inst/doc/ordinal-knee2.R | 252 +++++------
inst/doc/ordinal-retinopathy1.R | 254 +++++------
inst/doc/ordinal-retinopathy2.R | 306 ++++++-------
inst/doc/prediction-glass.R | 188 ++++----
inst/doc/prediction-medcare.R | 734 ++++++++++++++++-----------------
inst/doc/random-aids.R | 116 ++---
inst/doc/random-betablocker.R | 290 ++++++-------
inst/doc/random-knee1.R | 160 +++----
inst/doc/random-knee2.R | 176 +++----
inst/doc/random-knee3.R | 148 +++---
inst/doc/regsel-heartdisease1.R | 360 ++++++++--------
inst/doc/regsel-heartdisease2.R | 180 ++++----
inst/doc/regsel-heartdisease3.R | 226 +++++-----
inst/doc/regsel-heartdisease4.R | 182 ++++----
inst/doc/regsel-heartdisease5.R | 178 ++++----
inst/doc/regsel-heartdisease6.R | 298 ++++++-------
inst/doc/semiparametric-addiction.R | 290 ++++++-------
inst/doc/semiparametric-children.R | 88 +--
inst/doc/semiparametric-dust.R | 88 +--
inst/doc/semiparametric-unemployment.R | 214 ++++-----
inst/doc/tree-dust.R | 270 ++++++------
inst/doc/tree-unemployment.R | 142 +++---
man/retinopathy.Rd | 4
74 files changed, 4573 insertions(+), 4571 deletions(-)
Title: Fitting and Testing Generalized Logistic Distributions
Diff between glogis versions 0.1-1 dated 2014-02-20 and 1.0-0 dated 2014-11-11
Description: Tools for the generalized logistic distribution (Type I,
also known as skew-logistic distribution), encompassing
basic distribution functions (p, q, d, r, score), maximum
likelihood estimation, and structural change methods.
Author: Achim Zeileis [aut, cre],
Thomas Windberger [aut]
Maintainer: Achim Zeileis
glogis |only
1 file changed
Title: Random ferns classifier
Diff between rFerns versions 0.3.3 dated 2014-03-24 and 1.0.0 dated 2014-11-11
Description: An R implementation of the random ferns classifier by Ozuysal et al., modified for generic classification problems and featuring OOB error approximation and importance measure.
Author: Miron B. Kursa
Maintainer: Miron B. Kursa
DESCRIPTION | 6 +++---
MD5 | 13 +++++++------
inst/CITATION |only
inst/NEWS | 3 +++
man/rFerns.Rd | 4 ++--
src/ferns.c | 10 ++++++----
src/forest.h | 26 +++++++++++++++++---------
src/tools.h | 17 ++++++++++-------
8 files changed, 48 insertions(+), 31 deletions(-)
Title: Moment and Inverse Moment Bayes factors
Diff between mombf versions 1.5.7 dated 2014-04-04 and 1.5.9 dated 2014-11-11
Description: This package performs model selection based on non-local priors, including MOM, eMOM and iMOM priors. Routines are provided to compute Bayes factors, marginal densities and to perform variable selection in regression setups. Routines to evaluate prior densities, distribution functions, quantiles and modes are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell
ChangeLog | 11 ++++
DESCRIPTION | 11 ++--
MD5 | 38 +++++++-------
NAMESPACE | 2
R/AllGenerics.R | 2
R/cox.R |only
R/emomLM.R | 24 +++++++--
R/margpemom.R | 57 ++++++++++++----------
R/margpimom.R | 50 +++++++++++--------
R/margpmom.R | 57 +++++++++++++---------
R/modelSelection.R | 51 +++++++++++++++++++
R/rmom.R | 91 ++++++++++++++++++++++++++---------
build/vignette.rds |binary
data/hald.rda |binary
inst/doc/mombf.pdf |binary
man/eprod.Rd |only
man/rnlp.Rd | 34 +++++++++----
src/cstat.cpp | 136 +++++++++++++++++++++++++++++++++++++++++++++++------
src/cstat.h | 9 ++-
src/do_mombf.h | 2
src/modelSel.cpp | 58 +++++++---------------
21 files changed, 446 insertions(+), 187 deletions(-)
Title: Loading Google Adwords Data Into R
Diff between RAdwords versions 0.1 dated 2014-10-11 and 0.1.1 dated 2014-11-11
Description: The aim of RAdwords is loading Adwords data into R. Therefore the
package implements three main features. First, the package provides an
authentication process for R with the Adwords API via OAUTH2. Second, the
package offers an interface to apply the Adwords query language in R and
query the Adwords API with ad-hoc reports. Third, the received data are
transformed into suitable data formats for further data processing and data
analysis.
Author: Johannes Burkhardt
Maintainer: Johannes Burkhardt
DESCRIPTION | 8
MD5 | 89 +
R/getData.R | 7
R/transformData.R | 8
README.md | 10
inst/extdata/ACCOUNT_PERFORMANCE_REPORT.csv | 254 +++--
inst/extdata/ACCOUNT_REACH_FREQUENCY_REPORT.csv | 24
inst/extdata/ADGROUP_PERFORMANCE_REPORT.csv | 450 ++++++---
inst/extdata/ADGROUP_REACH_FREQUENCY_REPORT.csv | 54 -
inst/extdata/AD_EXTENSIONS_PERFORMANCE_REPORT.csv | 244 ++++-
inst/extdata/AD_PERFORMANCE_REPORT.csv | 412 ++++++--
inst/extdata/AGE_RANGE_PERFORMANCE_REPORT.csv | 261 ++++-
inst/extdata/AUDIENCE_PERFORMANCE_REPORT.csv | 280 ++++--
inst/extdata/AUTOMATIC_PLACEMENTS_PERFORMANCE_REPORT.csv | 212 +++-
inst/extdata/BID_GOAL_PERFORMANCE_REPORT.csv | 179 ++-
inst/extdata/BUDGET_PERFORMANCE_REPORT.csv | 94 +-
inst/extdata/CALL_METRICS_CALL_DETAILS_REPORT.csv | 49 -
inst/extdata/CAMPAIGN_AD_SCHEDULE_TARGET_REPORT.csv | 116 +-
inst/extdata/CAMPAIGN_LOCATION_TARGET_REPORT.csv | 119 +-
inst/extdata/CAMPAIGN_NEGATIVE_KEYWORDS_PERFORMANCE_REPORT.csv | 28
inst/extdata/CAMPAIGN_NEGATIVE_LOCATIONS_REPORT.csv | 14
inst/extdata/CAMPAIGN_NEGATIVE_PLACEMENTS_PERFORMANCE_REPORT.csv | 30
inst/extdata/CAMPAIGN_PERFORMANCE_REPORT.csv | 460 ++++++----
inst/extdata/CAMPAIGN_PLATFORM_TARGET_REPORT.csv | 126 +-
inst/extdata/CAMPAIGN_REACH_FREQUENCY_REPORT.csv | 39
inst/extdata/CAMPAIGN_SHARED_SET_REPORT.csv |only
inst/extdata/CLICK_PERFORMANCE_REPORT.csv | 163 ++-
inst/extdata/CREATIVE_CONVERSION_REPORT.csv | 94 +-
inst/extdata/CRITERIA_PERFORMANCE_REPORT.csv | 419 ++++++---
inst/extdata/DESTINATION_URL_REPORT.csv | 265 ++++-
inst/extdata/DISPLAY_KEYWORD_PERFORMANCE_REPORT.csv | 260 ++++-
inst/extdata/DISPLAY_TOPICS_PERFORMANCE_REPORT.csv | 261 ++++-
inst/extdata/GENDER_PERFORMANCE_REPORT.csv | 261 ++++-
inst/extdata/GEO_PERFORMANCE_REPORT.csv | 243 +++--
inst/extdata/KEYWORDLESS_CATEGORY_REPORT.csv | 154 ++-
inst/extdata/KEYWORDLESS_QUERY_REPORT.csv | 160 ++-
inst/extdata/KEYWORDS_PERFORMANCE_REPORT.csv | 438 ++++++---
inst/extdata/PAID_ORGANIC_QUERY_REPORT.csv | 58 -
inst/extdata/PLACEHOLDER_FEED_ITEM_REPORT.csv | 253 +++--
inst/extdata/PLACEHOLDER_REPORT.csv |only
inst/extdata/PLACEMENT_PERFORMANCE_REPORT.csv | 263 ++++-
inst/extdata/PRODUCT_PARTITION_REPORT.csv | 168 ++-
inst/extdata/SEARCH_QUERY_PERFORMANCE_REPORT.csv | 260 ++++-
inst/extdata/SHARED_SET_CRITERIA_REPORT.csv |only
inst/extdata/SHARED_SET_REPORT.csv |only
inst/extdata/SHOPPING_PERFORMANCE_REPORT.csv | 170 ++-
inst/extdata/URL_PERFORMANCE_REPORT.csv | 223 +++-
man/RAdwords.Rd |only
48 files changed, 5360 insertions(+), 2320 deletions(-)
Title: Accurate Estimation of Clonal Coincidences and Abundances from
Biological Replicates
Diff between lymphclon versions 1.2.3 dated 2013-11-11 and 1.3.0 dated 2014-11-11
Description: We provide a clonality score estimator that takes full advantage of the multi-biological-replicate structure of modern sequencing experiments; it specifically takes into account the reality that, typically, the clonal coverage is well below 0.1%.
Author: Yi Liu [aut, cre],
Richard A. Olshen [aut],
Andrew Z. Fire [ctb],
Scott D. Boyd [ctb]
Maintainer: Yi Liu
DESCRIPTION | 24 ++++++++++++------------
MD5 | 8 ++++----
NAMESPACE | 1 -
R/generate.clonal.data.R | 9 ++++++++-
man/lymphclon-package.Rd | 6 +++---
5 files changed, 27 insertions(+), 21 deletions(-)
Title: Discrete Bayesian Additive Regression Trees Sampler
Diff between dbarts versions 0.8-3 dated 2014-07-14 and 0.8-4 dated 2014-11-11
Description: Fits Bayesian additive regression trees (BART) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/MH sampler. Also serves as a drop-in replacement for package BayesTree.
Author: Hugh Chipman
Maintainer: Vincent Dorie
dbarts-0.8-3/dbarts/src/external/stats.c |only
dbarts-0.8-3/dbarts/tests/testthat/01-dbartsDataArgs.R |only
dbarts-0.8-3/dbarts/tests/testthat/02-dbartsModelArgs.R |only
dbarts-0.8-3/dbarts/tests/testthat/03-dbartsControl.R |only
dbarts-0.8-3/dbarts/tests/testthat/04-continuousResponse.R |only
dbarts-0.8-3/dbarts/tests/testthat/05-binaryResponse.R |only
dbarts-0.8-3/dbarts/tests/testthat/06-dbartsSampler.R |only
dbarts-0.8-4/dbarts/DESCRIPTION | 13
dbarts-0.8-4/dbarts/MD5 | 125
dbarts-0.8-4/dbarts/R/A_class.R | 39
dbarts-0.8-4/dbarts/R/bart.R | 20
dbarts-0.8-4/dbarts/R/data.R | 115
dbarts-0.8-4/dbarts/R/dbarts.R | 198
dbarts-0.8-4/dbarts/R/hooks.R | 6
dbarts-0.8-4/dbarts/README.md | 8
dbarts-0.8-4/dbarts/TODO | 6
dbarts-0.8-4/dbarts/cleanup | 4
dbarts-0.8-4/dbarts/configure | 2000 ++++++----
dbarts-0.8-4/dbarts/configure.ac | 16
dbarts-0.8-4/dbarts/inst/NEWS.Rd |only
dbarts-0.8-4/dbarts/inst/common/almostLinearBinaryData.R |only
dbarts-0.8-4/dbarts/inst/common/friedmanData.R | 6
dbarts-0.8-4/dbarts/inst/common/multithreadData.R |only
dbarts-0.8-4/dbarts/inst/include/dbarts/R_C_interface.hpp | 19
dbarts-0.8-4/dbarts/inst/include/dbarts/bartFit.hpp | 21
dbarts-0.8-4/dbarts/inst/include/dbarts/control.hpp | 9
dbarts-0.8-4/dbarts/inst/include/dbarts/data.hpp | 6
dbarts-0.8-4/dbarts/inst/include/dbarts/model.hpp | 9
dbarts-0.8-4/dbarts/inst/include/dbarts/state.hpp | 2
dbarts-0.8-4/dbarts/man/bart.Rd | 8
dbarts-0.8-4/dbarts/man/dbarts.Rd | 3
dbarts-0.8-4/dbarts/man/dbartsSampler-class.Rd | 20
dbarts-0.8-4/dbarts/src/Makevars.in | 21
dbarts-0.8-4/dbarts/src/Makevars.win | 8
dbarts-0.8-4/dbarts/src/R_C_interface.cpp | 39
dbarts-0.8-4/dbarts/src/R_interface.cpp | 432 +-
dbarts-0.8-4/dbarts/src/config.hpp.win | 8
dbarts-0.8-4/dbarts/src/dbarts/Makefile | 4
dbarts-0.8-4/dbarts/src/dbarts/bartFit.cpp | 417 +-
dbarts-0.8-4/dbarts/src/dbarts/birthDeathRule.cpp | 30
dbarts-0.8-4/dbarts/src/dbarts/changeRule.cpp | 36
dbarts-0.8-4/dbarts/src/dbarts/config.hpp.win | 16
dbarts-0.8-4/dbarts/src/dbarts/functions.cpp | 8
dbarts-0.8-4/dbarts/src/dbarts/node.cpp | 81
dbarts-0.8-4/dbarts/src/dbarts/node.hpp | 16
dbarts-0.8-4/dbarts/src/dbarts/parameterPrior.cpp | 13
dbarts-0.8-4/dbarts/src/dbarts/state.cpp | 8
dbarts-0.8-4/dbarts/src/dbarts/swapRule.cpp | 16
dbarts-0.8-4/dbarts/src/dbarts/tree.cpp | 56
dbarts-0.8-4/dbarts/src/dbarts/tree.hpp | 6
dbarts-0.8-4/dbarts/src/dbarts/treePrior.cpp | 22
dbarts-0.8-4/dbarts/src/external/Makefile | 20
dbarts-0.8-4/dbarts/src/external/config.h.in | 11
dbarts-0.8-4/dbarts/src/external/config.h.win | 11
dbarts-0.8-4/dbarts/src/external/linearAlgebra.c | 137
dbarts-0.8-4/dbarts/src/external/moments.c | 888 +++-
dbarts-0.8-4/dbarts/src/external/random.c |only
dbarts-0.8-4/dbarts/src/external/randomBase.c |only
dbarts-0.8-4/dbarts/src/external/randomNorm.c |only
dbarts-0.8-4/dbarts/src/external/thread.c | 33
dbarts-0.8-4/dbarts/src/include/external/alloca.h | 17
dbarts-0.8-4/dbarts/src/include/external/io.h | 9
dbarts-0.8-4/dbarts/src/include/external/linearAlgebra.h | 26
dbarts-0.8-4/dbarts/src/include/external/random.h |only
dbarts-0.8-4/dbarts/src/include/external/stats.h | 17
dbarts-0.8-4/dbarts/src/include/external/stddef.h | 18
dbarts-0.8-4/dbarts/src/include/external/thread.h | 5
dbarts-0.8-4/dbarts/tests/testthat/test-01-dbartsDataArgs.R |only
dbarts-0.8-4/dbarts/tests/testthat/test-02-dbartsModelArgs.R |only
dbarts-0.8-4/dbarts/tests/testthat/test-03-dbartsControl.R |only
dbarts-0.8-4/dbarts/tests/testthat/test-04-continuousResponse.R |only
dbarts-0.8-4/dbarts/tests/testthat/test-05-binaryResponse.R |only
dbarts-0.8-4/dbarts/tests/testthat/test-06-dbartsSampler.R |only
dbarts-0.8-4/dbarts/tests/testthat/test-07-bartMultithreaded.R |only
74 files changed, 3464 insertions(+), 1618 deletions(-)
Title: Tools for tensor analysis and decomposition
Diff between rTensor versions 1.1 dated 2014-04-08 and 1.2 dated 2014-11-11
Description: rTensor is a set of tools for creation, manipulation, and modeling
of tensors with arbitrary number of modes. A tensor in the context of data
analysis is a multidimensional array. rTensor does this by providing a S4
class 'Tensor' that wraps around the base 'array' class. rTensor also
provides common tensor operations as methods, including matrix unfolding,
summing/averaging across modes, calculating the Frobenius norm, and taking
the inner product between two tensors. Familiar array operations are
overloaded, such as index subsetting via '[' and element-wise operations.
rTensor also implements various tensor decomposition, including CP, GLRAM,
MPCA, PVD, and Tucker. For tensors with 3 modes, rTensor also implements
transpose, product, and SVD, as defined in Kilmer et al. (2013). Some
auxiliary functions include the Khatri-Rao product, Kronecker product, and
the Hamadard product for a list of matrices. Development of rTensor has
been generously supported by Cornell's Department of Statistical Science.
Author: James Li and Jacob Bien and Martin Wells
Maintainer: James Li
rTensor-1.1/rTensor/man/image-methods.Rd |only
rTensor-1.2/rTensor/DESCRIPTION | 11 -
rTensor-1.2/rTensor/MD5 | 94 ++++-----
rTensor-1.2/rTensor/NAMESPACE | 25 +-
rTensor-1.2/rTensor/NEWS | 12 +
rTensor-1.2/rTensor/R/rTensor_Class.R | 260 +++++++++++++-------------
rTensor-1.2/rTensor/R/rTensor_Decomp.R | 25 +-
rTensor-1.2/rTensor/R/rTensor_Misc.R | 96 ++++++---
rTensor-1.2/rTensor/man/Ops-methods.Rd | 16 +
rTensor-1.2/rTensor/man/Tensor-class.Rd | 150 +++++----------
rTensor-1.2/rTensor/man/as.tensor.Rd | 13 -
rTensor-1.2/rTensor/man/cp.Rd | 59 +----
rTensor-1.2/rTensor/man/cs_fold.Rd | 37 ---
rTensor-1.2/rTensor/man/cs_unfold-methods.Rd | 40 +---
rTensor-1.2/rTensor/man/dim-methods.Rd | 12 -
rTensor-1.2/rTensor/man/extract-methods.Rd | 26 +-
rTensor-1.2/rTensor/man/fnorm-methods.Rd | 14 +
rTensor-1.2/rTensor/man/fold.Rd | 37 +--
rTensor-1.2/rTensor/man/hamadard_list.Rd | 17 -
rTensor-1.2/rTensor/man/head-methods.Rd | 15 -
rTensor-1.2/rTensor/man/hosvd.Rd | 43 +---
rTensor-1.2/rTensor/man/initialize-methods.Rd | 19 +
rTensor-1.2/rTensor/man/innerProd-methods.Rd | 16 +
rTensor-1.2/rTensor/man/k_fold.Rd |only
rTensor-1.2/rTensor/man/k_unfold-methods.Rd |only
rTensor-1.2/rTensor/man/khatri_rao.Rd | 17 -
rTensor-1.2/rTensor/man/khatri_rao_list.Rd | 18 -
rTensor-1.2/rTensor/man/kronecker_list.Rd | 14 -
rTensor-1.2/rTensor/man/matvec-methods.Rd |only
rTensor-1.2/rTensor/man/modeMean-methods.Rd | 22 +-
rTensor-1.2/rTensor/man/modeSum-methods.Rd | 21 +-
rTensor-1.2/rTensor/man/mpca.Rd | 62 ++----
rTensor-1.2/rTensor/man/print-methods.Rd | 15 -
rTensor-1.2/rTensor/man/pvd.Rd | 56 +----
rTensor-1.2/rTensor/man/rTensor-package.Rd | 4
rTensor-1.2/rTensor/man/rand_tensor.Rd | 16 -
rTensor-1.2/rTensor/man/rs_fold.Rd | 37 ---
rTensor-1.2/rTensor/man/rs_unfold-methods.Rd | 34 +--
rTensor-1.2/rTensor/man/show-methods.Rd | 15 -
rTensor-1.2/rTensor/man/t-methods.Rd | 18 -
rTensor-1.2/rTensor/man/t_mult.Rd | 24 --
rTensor-1.2/rTensor/man/t_svd.Rd | 35 +--
rTensor-1.2/rTensor/man/t_svd_reconstruct.Rd | 12 -
rTensor-1.2/rTensor/man/tail-methods.Rd | 15 -
rTensor-1.2/rTensor/man/tperm-methods.Rd | 16 +
rTensor-1.2/rTensor/man/ttl.Rd | 37 +--
rTensor-1.2/rTensor/man/ttm.Rd | 32 +--
rTensor-1.2/rTensor/man/tucker.Rd | 65 ++----
rTensor-1.2/rTensor/man/unfold-methods.Rd | 44 +---
rTensor-1.2/rTensor/man/unmatvec.Rd |only
rTensor-1.2/rTensor/man/vec-methods.Rd |only
51 files changed, 754 insertions(+), 912 deletions(-)
Title: Quality Improvement Charts
Diff between qicharts versions 0.1.0 dated 2014-10-07 and 0.1.1 dated 2014-11-11
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic, creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej
DESCRIPTION | 24
MD5 | 27
NEWS | 15
R/qic.R | 1975 ++++++++++++++++++++++++------------------------
R/trc.R | 54 -
README.md | 53 -
build/vignette.rds |binary
inst/doc/runcharts.Rmd | 8
inst/doc/runcharts.html | 26
man/trc.Rd | 21
vignettes/figure |only
vignettes/runcharts.Rmd | 8
12 files changed, 1130 insertions(+), 1081 deletions(-)
Title: Phylogenetic analysis in R
Diff between phangorn versions 1.99-9 dated 2014-10-09 and 1.99-11 dated 2014-11-11
Description: Phylogenetic analysis in R (Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
Distance methods & Hadamard conjugation)
Author: Klaus Schliep, Emmanuel Paradis
Maintainer: Klaus Schliep
DESCRIPTION | 8
MD5 | 154
NAMESPACE | 156
NEWS | 1640 +++---
R/Coalescent.R | 196
R/Densi.R | 398 -
R/SOWH.R | 117
R/cladePar.R | 38
R/clanistic.R | 824 +--
R/dist.p.R | 158
R/distSeq.R | 388 -
R/fitch.R | 1056 ++--
R/networx.R | 2421 +++++-----
R/parsimony.R | 1660 +++---
R/phyDat.R | 1578 +++---
R/phylo.R | 9621 +++++++++++++++++++---------------------
R/sankoff.R | 190
R/simSeq.R | 170
R/treeManipulation.R | 2102 ++++----
R/treedist.R | 584 +-
R/zzz.R | 19
README.md | 34
build/vignette.rds |binary
inst/CITATION | 34
inst/README | 44
inst/doc/Ancestral.R | 220
inst/doc/Ancestral.Rnw | 340 -
inst/doc/Trees.R | 442 -
inst/doc/Trees.Rnw | 510 +-
inst/doc/phangorn-specials.R | 218
inst/doc/phangorn-specials.Rnw | 514 +-
inst/extdata/Blosum62.dat | 44
inst/extdata/Dayhoff.dat | 44
inst/extdata/HIVb.dat | 44
inst/extdata/HIVw.dat | 44
inst/extdata/JTT.dat | 44
inst/extdata/MtZoa.dat | 60
inst/extdata/RtREV.dat | 44
inst/extdata/VT.dat | 44
inst/extdata/mtREV24.dat | 78
inst/extdata/mtmam.dat | 154
man/Ancestors.Rd | 98
man/NJ.Rd | 84
man/SH.test.Rd | 96
man/SOWH.test.Rd | 100
man/ancestral.pml.Rd | 142
man/as.splits.Rd | 154
man/bab.Rd | 126
man/bootstrap.pml.Rd | 208
man/cladePar.Rd | 126
man/consensusNet.Rd | 112
man/densiTree.Rd | 168
man/dist.hamming.Rd | 98
man/dist.p.Rd | 142
man/getClans.Rd | 244 -
man/hadamard.Rd | 162
man/lento.Rd | 94
man/midpoint.Rd | 100
man/modelTest.Rd | 134
man/nni.Rd | 72
man/parsimony.Rd | 162
man/plot.networx.Rd | 231
man/pml.Rd | 304 -
man/pml.fit.Rd | 158
man/pmlCluster.Rd | 132
man/pmlMix.Rd | 206
man/pmlPart.Rd | 134
man/simSeq.Rd | 148
man/splitsNetwork.Rd | 110
man/superTree.Rd | 140
man/treedist.Rd | 92
src/fitch.c | 7
src/ml.c | 6
vignettes/Ancestral.Rnw | 340 -
vignettes/Trees.Rnw | 510 +-
vignettes/phangorn-specials.Rnw | 514 +-
vignettes/phangorn.bib | 588 +-
vignettes/primates.dna | 122
78 files changed, 16420 insertions(+), 16378 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Diff between knitr versions 1.7 dated 2014-10-13 and 1.8 dated 2014-11-11
Description: This package provides a general-purpose tool for dynamic report
generation in R, which can be used to deal with any type of (plain text)
files, including Sweave, HTML, Markdown, reStructuredText, AsciiDoc, and
Textile. R code is evaluated as if it were copied and pasted in an R
terminal thanks to the evaluate package (e.g., we do not need to explicitly
print() plots from ggplot2 or lattice). R code can be reformatted by the
formatR package so that long lines are automatically wrapped, with indent
and spaces added, and comments preserved. A simple caching mechanism is
provided to cache results from computations for the first time and the
computations will be skipped the next time. Almost all common graphics
devices, including those in base R and add-on packages like Cairo,
cairoDevice and tikzDevice, are built-in with this package and it is
straightforward to switch between devices without writing any special
functions. The width and height as well as alignment of plots in the output
document can be specified in chunk options (the size of plots for graphics
devices is also supported). Multiple plots can be recorded in a single code
chunk, and it is also allowed to rearrange plots to the end of a chunk or
just keep the last plot. Warnings, messages and errors are written in the
output document by default (can be turned off). The large collection of
hooks in this package makes it possible for the user to control almost
everything in the R code input and output. Hooks can be used either to
format the output or to run R code fragments before or after a code chunk.
The language in code chunks is not restricted to R (there is simple support
to Python and shell scripts, etc). Many features are borrowed from or
inspired by Sweave, cacheSweave, pgfSweave, brew and decumar.
Author: Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Ashley Manton [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jeff Arnold [ctb],
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
John Honaker [ctb],
Jonathan Keane [ctb],
J.J. Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Romain Francois [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie
DESCRIPTION | 108 +-
MD5 | 101 +-
NAMESPACE | 5
NEWS | 1943 ---------------------------------------
R/cache.R | 10
R/defaults.R | 2
R/engine.R | 38
R/highlight.R | 3
R/hooks-extra.R | 2
R/hooks-html.R | 20
R/hooks-latex.R | 29
R/hooks-md.R | 22
R/output.R | 2
R/parser.R | 65 +
R/spin.R | 35
R/table.R | 41
R/template.R | 25
R/themes-eclipse.R | 2
R/utils-conversion.R | 7
R/utils-rd2html.R | 8
R/utils-vignettes.R | 48
R/utils.R | 47
build/knitr.pdf |binary
build/vignette.rds |binary
inst/doc/datatables.html | 6
inst/doc/docco-classic.html | 10
inst/doc/docco-linear.html | 10
inst/doc/knit_expand.html | 4
inst/doc/knit_print.html | 169 +--
inst/doc/knitr-intro.html | 53 -
inst/doc/knitr-markdown.html | 2
inst/doc/knitr-refcard.pdf |binary
inst/examples/knitr-packages.bib | 38
inst/misc/datatables.html | 6
inst/misc/docco-classic.html | 10
inst/misc/docco-template.html | 10
inst/misc/knitr-template.Rnw | 1
inst/misc/toggleR.js | 13
inst/opencpu/apps/index.html | 12
inst/shiny/server.R | 2
inst/shiny/ui.R | 8
man/eclipse_theme.Rd | 2
man/engine_output.Rd |only
man/fig_chunk.Rd |only
man/inline_expr.Rd |only
man/kable.Rd | 10
man/knit_filter.Rd |only
man/knit_rd.Rd | 2
man/rand_seed.Rd | 4
man/read_rforge.Rd | 2
man/spin_child.Rd |only
man/stitch.Rd | 10
tests/testit/test-table.R | 51 +
tests/testit/test-utils.R | 10
54 files changed, 699 insertions(+), 2309 deletions(-)