Title: Regression Spline Functions and Classes
Description: Constructs B-splines and its integral, monotone splines
(M-splines) and its integral (I-splines), convex splines (C-splines),
and their derivatives of given order. Piecewise constant basis is
allowed for B-splines and M-splines. See
De Boor (1978) <doi:10.1002/zamm.19800600129>,
Ramsay (1988) <doi:10.1214/ss/1177012761>, and
Meyer (2008) <doi:10.1214/08-AOAS167> for more information.
Author: Wenjie Wang [aut, cre],
Jun Yan [aut]
Maintainer: Wenjie Wang <wenjie.2.wang@uconn.edu>
Diff between splines2 versions 0.2.5 dated 2017-02-10 and 0.2.6 dated 2017-09-11
DESCRIPTION | 18 +++++---- MD5 | 27 +++++++------- NEWS.md | 10 ++++- R/bSpline.R | 77 ++++++++++++++++++++++++++++++++---------- R/dbs.R | 3 - R/misc.R |only README.md | 9 ++-- build/vignette.rds |binary inst/CITATION | 8 ++-- inst/bib/splines2.bib | 9 +++- inst/doc/splines2-intro.Rmd | 8 ++-- inst/doc/splines2-intro.html | 28 +++++++-------- tests/testthat/test-bSpline.R | 4 ++ tests/testthat/test-cSpline.R | 2 - vignettes/splines2-intro.Rmd | 8 ++-- 15 files changed, 135 insertions(+), 76 deletions(-)
Title: Nelson-Aalen Estimator of the Cumulative Hazard in Multistate
Models
Description: Computes the Nelson-Aalen estimator of the cumulative transition hazard for arbitrary Markov multistate models <ISBN:978-0-387-68560-1>.
Author: Arthur Allignol
Maintainer: Arthur Allignol <arthur.allignol@gmail.com>
Diff between mvna versions 2.0 dated 2017-01-13 and 2.0.1 dated 2017-09-11
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NAMESPACE | 2 +- man/lines.mvna.Rd | 2 +- man/mvna.Rd | 2 +- man/plot.mvna.Rd | 2 +- man/predict.mvna.Rd | 2 +- man/summary.mvna.Rd | 2 +- src/init.c |only 9 files changed, 18 insertions(+), 17 deletions(-)
Title: Interface Between GMT Map-Making Software and R
Description: Interface between the GMT map-making software and R, enabling the
user to manipulate geographic data within R and call GMT commands to draw and
annotate maps in postscript format. The gmt package is about interactive data
analysis, rapidly visualizing subsets and summaries of geographic data, while
performing statistical analysis in the R console.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between gmt versions 2.0-0 dated 2017-06-20 and 2.0-1 dated 2017-09-11
DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++------- NEWS | 8 ++++++++ README.md |only data/demo.bar.rda |binary data/demo.coast.rda |binary data/demo.par.rda |binary data/demo.text.rda |binary data/demo.xy.rda |binary 9 files changed, 21 insertions(+), 12 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging and a distance based on global alignment kernels
are also provided. All included distance functions have custom loops
optimized for the calculation of cross-distance matrices, including
parallelization support. Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 4.1.0 dated 2017-09-11 and 4.1.1 dated 2017-09-11
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/partitional.R | 2 +- inst/NEWS.Rd | 32 ++++++++++++++++---------------- inst/doc/dtwclust.pdf |binary 5 files changed, 24 insertions(+), 24 deletions(-)
Title: Conditioned Latin Hypercube Sampling
Description: Conditioned Latin hypercube sampling, as published by Minasny and McBratney (2006) <DOI:10.1016/j.cageo.2005.12.009>. This method proposes to stratify sampling in presence of ancillary data. An extension of this method, which propose to associate a cost to each individual and take it into account during the optimisation process, is also proposed (Roudier et al., 2012, <DOI:10.1201/b12728-46>).
Author: Pierre Roudier
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
Diff between clhs versions 0.5-6 dated 2016-10-13 and 0.5-7 dated 2017-09-11
clhs-0.5-6/clhs/inst/doc/vignette.R |only clhs-0.5-6/clhs/inst/doc/vignette.Rnw |only clhs-0.5-6/clhs/inst/doc/vignette.pdf |only clhs-0.5-6/clhs/vignettes/vignette.Rnw |only clhs-0.5-7/clhs/DESCRIPTION | 11 +++++--- clhs-0.5-7/clhs/MD5 | 16 ++++++------ clhs-0.5-7/clhs/NEWS | 3 ++ clhs-0.5-7/clhs/R/clhs.R | 40 ++++++++++++++++++++----------- clhs-0.5-7/clhs/build/vignette.rds |binary clhs-0.5-7/clhs/inst/doc/intro-clhs.R |only clhs-0.5-7/clhs/inst/doc/intro-clhs.Rmd |only clhs-0.5-7/clhs/inst/doc/intro-clhs.html |only clhs-0.5-7/clhs/vignettes/intro-clhs.Rmd |only 13 files changed, 45 insertions(+), 25 deletions(-)
Title: A Graphical User Interface for the 'yuima' Package
Description: Provides a graphical user interface for the 'yuima' package.
Author: YUIMA Project Team
Maintainer: Emanuele Guidotti <emanuele.guidotti@studenti.unimi.it>
Diff between yuimaGUI versions 1.1.0 dated 2017-05-10 and 1.2.0 dated 2017-09-11
yuimaGUI-1.1.0/yuimaGUI/inst/yuimaGUI/ui/simulation/simulate.R |only yuimaGUI-1.2.0/yuimaGUI/DESCRIPTION | 8 yuimaGUI-1.2.0/yuimaGUI/MD5 | 40 yuimaGUI-1.2.0/yuimaGUI/NAMESPACE | 3 yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/global.R | 12 yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server.R | 14 yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server/functions.R | 408 ++++++---- yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server/modeling/multivariate_results.R |only yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server/modeling/multivariate_start_estimation.R | 300 +++---- yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server/modeling/univariate_results.R | 7 yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server/modeling/univariate_start_estimation.R | 2 yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server/settings.R | 71 + yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server/simulation/multivariate_estimated.R |only yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server/simulation/multivariate_non_estimated.R |only yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server/simulation/multivariate_results.R |only yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server/simulation/univariate_estimated.R | 6 yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/server/simulation/univariate_non_estimated.R | 7 yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/ui.R | 33 yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/ui/load_data/finData.R | 2 yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/ui/modeling/multi_models.R | 68 - yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/ui/simulation/multivariate.R |only yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/ui/simulation/univariate.R |only yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/www/black.css | 42 - yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/www/white.css | 40 yuimaGUI-1.2.0/yuimaGUI/inst/yuimaGUI/www/yuimaLogo.ico |only 25 files changed, 648 insertions(+), 415 deletions(-)
Title: Tide Analysis and Prediction of Predominantly Semi-Diurnal Tides
Description: Tide analysis and prediction of predominantly semi-diurnal tides
with two high waters and two low waters during one lunar day (~24.842 hours,
~1.035 days). The analysis should preferably cover an observation period of at
least 19 years. For shorter periods, for example, the nodal cycle can not be
taken into account, which particularly affects the height calculation. The main
objective of this package is to produce tide tables.
Author: Moritz Mueller-Navarra [aut, cre],
Sylvin Mueller-Navarra [aut],
Andreas Boesch [ctb]
Maintainer: Moritz Mueller-Navarra <muellernavarra@gmail.com>
Diff between TideTables versions 0.0.1 dated 2015-12-01 and 0.0.2 dated 2017-09-11
DESCRIPTION | 16 +- MD5 | 22 ++- NAMESPACE | 3 NEWS |only R/TideTable.R | 152 +++++++++++++------------ R/UtilityFunctions.R | 306 +++++++++++++++++++++++++++++++++++++-------------- R/observation.R | 4 man/EstimateTmhwi.Rd |only man/Funcs.Rd | 15 -- man/NumCulm.Rd | 3 man/PlotTides.Rd | 3 man/TideTable.Rd | 7 - man/observation.Rd | 3 13 files changed, 339 insertions(+), 195 deletions(-)
Title: Analysis and Prediction of Tides
Description: Tidal analysis of evenly spaced observed time series (time step 1 to 60 min) with or
without shorter gaps.
The analysis should preferably cover an observation period of at least 19 years.
For shorter periods low frequency constituents are not taken into account, in accordance with the Rayleigh-Criterion.
The main objective of this package is to synthesize or predict a tidal time series.
Author: Moritz Mueller-Navarra [aut, cre], Sylvin Mueller-Navarra [aut], Andreas Boesch [aut]
Maintainer: Moritz Mueller-Navarra <muellernavarra@gmail.com>
Diff between TideCurves versions 0.0.2 dated 2017-06-03 and 0.0.3 dated 2017-09-11
TideCurves-0.0.2/TideCurves/R/PlotTideCurve.R |only TideCurves-0.0.2/TideCurves/man/PlotTideCurve.Rd |only TideCurves-0.0.3/TideCurves/DESCRIPTION | 8 TideCurves-0.0.3/TideCurves/MD5 | 18 -- TideCurves-0.0.3/TideCurves/NAMESPACE | 5 TideCurves-0.0.3/TideCurves/NEWS | 11 + TideCurves-0.0.3/TideCurves/R/Funcs.R | 202 ++++++++++++++--------- TideCurves-0.0.3/TideCurves/R/TideCurve.R | 15 - TideCurves-0.0.3/TideCurves/README.md | 2 TideCurves-0.0.3/TideCurves/man/Funcs.Rd | 12 - TideCurves-0.0.3/TideCurves/man/TideCurve.Rd | 4 11 files changed, 164 insertions(+), 113 deletions(-)
Title: An 'SVG' Graphics Device
Description: A graphics device for R that produces 'Scalable Vector Graphics'.
'svglite' is a fork of the older 'RSvgDevice' package.
Author: Hadley Wickham [aut],
Lionel Henry [aut, cre],
T Jake Luciani [aut],
Matthieu Decorde [aut],
Vaudor Lise [aut],
Tony Plate [ctb] (Early line dashing code),
David Gohel [ctb] (Line dashing code and raster code),
Yixuan Qiu [ctb] (Improved styles; polypath implementation),
Håkon Malmedal [ctb] (Opacity code),
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between svglite versions 1.2.0 dated 2016-11-03 and 1.2.1 dated 2017-09-11
DESCRIPTION | 14 +++++++------- MD5 | 28 ++++++++++++++-------------- NEWS.md | 6 ++++++ R/RcppExports.R | 6 +++--- README.md | 4 +++- build/vignette.rds |binary inst/doc/fonts.html | 8 ++++---- inst/doc/scaling.html | 8 ++++---- man/editSVG.Rd | 1 - man/htmlSVG.Rd | 1 - man/stringSVG.Rd | 1 - man/svglite.Rd | 11 +++++------ man/svgstring.Rd | 1 - man/xmlSVG.Rd | 1 - src/RcppExports.cpp | 18 +++++++++++++++--- 15 files changed, 61 insertions(+), 47 deletions(-)
Title: Regression Standardization
Description: Contains functionality for regression standardization.
Three general classes of models are allowed; generalized linear models,
Cox proportional hazards models and shared frailty gamma-Weibull models.
Author: Arvid Sjolander and Elisabeth Dahlqwist
Maintainer: Arvid Sjolander <arvid.sjolander@ki.se>
Diff between stdReg versions 2.1 dated 2017-02-03 and 2.2.0 dated 2017-09-11
DESCRIPTION | 15 MD5 | 40 +- NAMESPACE | 3 R/sourcecode.R | 613 +++++++++++++++++++------------------ build/partial.rdb |binary man/CI.Rd |only man/delmet.Rd |only man/parfrailty.rd | 98 ++--- man/plot.stdCoxph.Rd | 38 -- man/plot.stdGlm.Rd | 35 -- man/plot.stdParfrailty.rd | 43 -- man/print.summary.parfrailty.rd | 20 - man/print.summary.stdCoxph.Rd | 17 - man/print.summary.stdGlm.Rd | 17 - man/print.summary.stdParfrailty.rd | 17 - man/stdCoxph.Rd | 47 +- man/stdGlm.Rd | 56 +-- man/stdParfrailty.rd | 69 +--- man/summary.parfrailty.rd | 26 - man/summary.stdCoxph.Rd | 35 -- man/summary.stdGlm.Rd | 34 -- man/summary.stdParfrailty.rd | 37 -- 22 files changed, 596 insertions(+), 664 deletions(-)
Title: Nested and Crossed Block Designs for Factorial, Fractional
Factorial and Unstructured Treatment Sets
Description: The 'blocksdesign' package constructs nested block and
D-optimal factorial designs for any unstructured or factorial
treatment model of any size. The nested block designs can have repeated
nesting down to any required depth of nesting with either a simple set
of nested blocks or a crossed row-and-column blocks design at each level
of nesting. The block design at each level of nesting is optimized for
D-efficiency within the blocks of each preceding set of
blocks. The block sizes in any particular block classification are always
as nearly equal as possible and never differ by more than a single plot.
Outputs include a table showing the allocation of
treatments to blocks, a plan layout showing the allocation of treatments
within blocks (unstructured treatment designs only) the achieved
D and A-efficiency factors for the block and treatment design
(factorial treatment designs only) and, where feasible,
an A-efficiency upper bound for the block design (unstructured
treatment designs only).
Author: R. N. Edmondson.
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 2.6 dated 2017-07-18 and 2.7 dated 2017-09-11
DESCRIPTION | 40 - MD5 | 18 NAMESPACE | 20 R/blocks.r | 1336 ++++++++++++++++++++++---------------------- R/blocksdesign-package.r | 18 R/factblocks.r | 1297 +++++++++++++++++++++--------------------- man/blocks.Rd | 301 ++++----- man/blocksdesign-package.Rd | 116 +-- man/factblocks.Rd | 314 +++++----- man/upper_bounds.Rd | 66 +- 10 files changed, 1762 insertions(+), 1764 deletions(-)
Title: Bayesian Analysis of Censored Regression Models Under Scale
Mixture of Skew Normal Distributions
Description: Propose a parametric fit for censored linear regression models based on SMSN distributions, from a Bayesian perspective. Also, generates SMSN random variables.
Author: Aldo M. Garay <medina_garay@yahoo.com>, Monique B. Massuia <moniquemassuia@gmail.com>, Victor H. Lachos <hlachos@ime.unicamp.br>, Eraldo B. Anjos Filho <ebdaf1@de.ufpe.br>
Maintainer: Aldo M. Garay <medina_garay@yahoo.com>
Diff between BayesCR versions 2.0 dated 2015-01-31 and 2.1 dated 2017-09-11
BayesCR-2.0/BayesCR/R/Criterios.R |only BayesCR-2.0/BayesCR/R/GibbsAssim.R |only BayesCR-2.0/BayesCR/R/GibbsSim.r |only BayesCR-2.0/BayesCR/R/SMSNloglik.r |only BayesCR-2.0/BayesCR/R/UtilitariosAssim.R |only BayesCR-2.0/BayesCR/R/UtilitariosSim.r |only BayesCR-2.0/BayesCR/R/gerarSMSN.R |only BayesCR-2.0/BayesCR/data/motorettes.txt.gz |only BayesCR-2.1/BayesCR/DESCRIPTION | 22 BayesCR-2.1/BayesCR/MD5 | 30 - BayesCR-2.1/BayesCR/NAMESPACE | 44 + BayesCR-2.1/BayesCR/R/Bayes.CR.r | 799 +++++++++++++++-------------- BayesCR-2.1/BayesCR/R/BayesCR.R |only BayesCR-2.1/BayesCR/R/gibbs_assim.R |only BayesCR-2.1/BayesCR/R/gibbs_sim.r |only BayesCR-2.1/BayesCR/R/motorettes.R |only BayesCR-2.1/BayesCR/R/rSMSN.R |only BayesCR-2.1/BayesCR/R/utility.R |only BayesCR-2.1/BayesCR/R/utility_assim.R |only BayesCR-2.1/BayesCR/R/utility_sim.r |only BayesCR-2.1/BayesCR/data/motorettes.rda |only BayesCR-2.1/BayesCR/man/Bayes.CR.Rd | 142 +++-- BayesCR-2.1/BayesCR/man/BayesCR.Rd |only BayesCR-2.1/BayesCR/man/motorettes.Rd | 52 - BayesCR-2.1/BayesCR/man/rSMSN.Rd | 70 +- 25 files changed, 652 insertions(+), 507 deletions(-)
Title: Tools for Healthcare Machine Learning
Description: A machine learning toolbox tailored to healthcare data.
Aids in data cleaning, model development, hyperparameter tuning, and model
deployment in a production SQL environment. Algorithms currently supported
are Lasso, Random Forest, XGBoost, Kmeans clustering, and Linear Mixed Model.
Author: Levi Thatcher [aut, cre],
Mike Mastanduno [aut],
Michael Levy [aut],
Taylor Miller [aut],
Taylor Larsen [aut]
Maintainer: Levi Thatcher <levi.thatcher@healthcatalyst.com>
Diff between healthcareai versions 0.1.12 dated 2017-05-04 and 1.0.0 dated 2017-09-11
healthcareai-0.1.12/healthcareai/R/common.R |only healthcareai-0.1.12/healthcareai/R/feature-availability-profiler.R |only healthcareai-0.1.12/healthcareai/inst/RMarkdown |only healthcareai-0.1.12/healthcareai/tests/testthat/rmodel_combined.rda |only healthcareai-0.1.12/healthcareai/tests/testthat/rmodel_probability.rda |only healthcareai-0.1.12/healthcareai/tests/testthat/rmodel_var_import.rda |only healthcareai-0.1.12/healthcareai/tests/testthat/test-deploy-supervised-model.R |only healthcareai-0.1.12/healthcareai/tests/testthat/test-deploy-to-df.R |only healthcareai-0.1.12/healthcareai/tests/testthat/test-deploy-to-sql.R |only healthcareai-0.1.12/healthcareai/tests/testthat/test-impute-column.r |only healthcareai-1.0.0/healthcareai/DESCRIPTION | 18 healthcareai-1.0.0/healthcareai/LICENSE | 4 healthcareai-1.0.0/healthcareai/MD5 | 292 - healthcareai-1.0.0/healthcareai/NAMESPACE | 154 healthcareai-1.0.0/healthcareai/R/common-LIME-like.R |only healthcareai-1.0.0/healthcareai/R/common-column-row-expectations.R |only healthcareai-1.0.0/healthcareai/R/common-connections.R |only healthcareai-1.0.0/healthcareai/R/common-correlations.R |only healthcareai-1.0.0/healthcareai/R/common-count-missing-data.R |only healthcareai-1.0.0/healthcareai/R/common-date-time.R |only healthcareai-1.0.0/healthcareai/R/common-feature-availability-profiler.R |only healthcareai-1.0.0/healthcareai/R/common-find-trends.R |only healthcareai-1.0.0/healthcareai/R/common-find-variation.R |only healthcareai-1.0.0/healthcareai/R/common-impute.R |only healthcareai-1.0.0/healthcareai/R/common-kmeans.R |only healthcareai-1.0.0/healthcareai/R/common-model-performance.R |only healthcareai-1.0.0/healthcareai/R/common-plot.R |only healthcareai-1.0.0/healthcareai/R/common-row-ordering.R |only healthcareai-1.0.0/healthcareai/R/common-testing-utils.R |only healthcareai-1.0.0/healthcareai/R/common-utilities.R |only healthcareai-1.0.0/healthcareai/R/healthcareai.R | 163 healthcareai-1.0.0/healthcareai/R/kmeans-clustering-method.R |only healthcareai-1.0.0/healthcareai/R/lasso-deployment.R | 1033 ++--- healthcareai-1.0.0/healthcareai/R/lasso-development.R | 812 ++-- healthcareai-1.0.0/healthcareai/R/linear-mixed-model-deployment.R | 1144 ++--- healthcareai-1.0.0/healthcareai/R/linear-mixed-model-development.R | 862 ++-- healthcareai-1.0.0/healthcareai/R/random-forest-deployment.R | 1089 ++--- healthcareai-1.0.0/healthcareai/R/random-forest-development.R | 983 ++-- healthcareai-1.0.0/healthcareai/R/risk-adjusted-comparisons.R | 308 - healthcareai-1.0.0/healthcareai/R/supervised-model-deployment-params.R | 82 healthcareai-1.0.0/healthcareai/R/supervised-model-deployment.R | 856 ++-- healthcareai-1.0.0/healthcareai/R/supervised-model-development-params.R | 89 healthcareai-1.0.0/healthcareai/R/supervised-model-development.R | 807 ++-- healthcareai-1.0.0/healthcareai/R/unsupervised-model-params.R | 56 healthcareai-1.0.0/healthcareai/R/unsupervised-model.R | 358 + healthcareai-1.0.0/healthcareai/R/xgboost-deployment.R |only healthcareai-1.0.0/healthcareai/R/xgboost-development.R |only healthcareai-1.0.0/healthcareai/README.md | 291 - healthcareai-1.0.0/healthcareai/inst/docs/clustering |only healthcareai-1.0.0/healthcareai/inst/docs/comparing-and-deploying/compare.html |only healthcareai-1.0.0/healthcareai/inst/docs/comparing-and-deploying/compare.md | 472 +- healthcareai-1.0.0/healthcareai/inst/docs/comparing-and-deploying/deploy.html |only healthcareai-1.0.0/healthcareai/inst/docs/comparing-and-deploying/deploy.md | 621 +-- healthcareai-1.0.0/healthcareai/inst/docs/comparing-and-deploying/evaluate-in-the-wild.md | 112 healthcareai-1.0.0/healthcareai/inst/docs/getting-started/FAQ-and-contact.md | 48 healthcareai-1.0.0/healthcareai/inst/docs/getting-started/profiling-your-data.md | 118 healthcareai-1.0.0/healthcareai/inst/docs/getting-started/where-do-i-begin.md | 32 healthcareai-1.0.0/healthcareai/inst/docs/healthcare-statistics/find-all-correlations.md | 102 healthcareai-1.0.0/healthcareai/inst/docs/healthcare-statistics/find-targeted-correlations.md | 112 healthcareai-1.0.0/healthcareai/inst/docs/healthcare-statistics/find-variation.md |only healthcareai-1.0.0/healthcareai/inst/docs/healthcare-statistics/img |only healthcareai-1.0.0/healthcareai/inst/docs/healthcare-statistics/risk-adjusted-comparisons.md | 233 - healthcareai-1.0.0/healthcareai/inst/docs/healthcare-statistics/trend-analysis.md | 134 healthcareai-1.0.0/healthcareai/inst/docs/healthcare-statistics/variation-across-groups.md |only healthcareai-1.0.0/healthcareai/inst/docs/index.md | 221 - healthcareai-1.0.0/healthcareai/inst/docs/model-pre-processing/feature-eng-overview.md | 22 healthcareai-1.0.0/healthcareai/inst/docs/model-pre-processing/longitudinal-imputation.md | 128 healthcareai-1.0.0/healthcareai/inst/docs/model-pre-processing/seasonality-handling.md | 100 healthcareai-1.0.0/healthcareai/inst/extdata/HCRDiabetesClinical.csv | 2002 +++++----- healthcareai-1.0.0/healthcareai/inst/extdata/dermatology_multiclass_data.csv |only healthcareai-1.0.0/healthcareai/inst/extdata/unit-test.sqlite |binary healthcareai-1.0.0/healthcareai/man/KmeansClustering.Rd |only healthcareai-1.0.0/healthcareai/man/LassoDeployment.Rd | 645 ++- healthcareai-1.0.0/healthcareai/man/LassoDevelopment.Rd | 418 +- healthcareai-1.0.0/healthcareai/man/LinearMixedModelDeployment.Rd | 672 ++- healthcareai-1.0.0/healthcareai/man/LinearMixedModelDevelopment.Rd | 484 +- healthcareai-1.0.0/healthcareai/man/RandomForestDeployment.Rd | 646 ++- healthcareai-1.0.0/healthcareai/man/RandomForestDevelopment.Rd | 455 +- healthcareai-1.0.0/healthcareai/man/RiskAdjustedComparisons.Rd | 149 healthcareai-1.0.0/healthcareai/man/SupervisedModelDeployment.Rd | 48 healthcareai-1.0.0/healthcareai/man/SupervisedModelDeploymentParams.Rd | 44 healthcareai-1.0.0/healthcareai/man/SupervisedModelDevelopment.Rd | 48 healthcareai-1.0.0/healthcareai/man/SupervisedModelDevelopmentParams.Rd | 42 healthcareai-1.0.0/healthcareai/man/UnsupervisedModel.Rd |only healthcareai-1.0.0/healthcareai/man/UnsupervisedModelParams.Rd |only healthcareai-1.0.0/healthcareai/man/XGBoostDeployment.Rd |only healthcareai-1.0.0/healthcareai/man/XGBoostDevelopment.Rd |only healthcareai-1.0.0/healthcareai/man/addSAMUtilityCols.Rd |only healthcareai-1.0.0/healthcareai/man/assignClusterLabels.Rd |only healthcareai-1.0.0/healthcareai/man/calculateAllCorrelations.Rd | 66 healthcareai-1.0.0/healthcareai/man/calculateCOV.Rd |only healthcareai-1.0.0/healthcareai/man/calculateConfusion.Rd |only healthcareai-1.0.0/healthcareai/man/calculateHourBins.Rd | 58 healthcareai-1.0.0/healthcareai/man/calculatePerformance.Rd | 60 healthcareai-1.0.0/healthcareai/man/calculateSDChanges.Rd | 84 healthcareai-1.0.0/healthcareai/man/calculateTargetedCorrelations.Rd | 74 healthcareai-1.0.0/healthcareai/man/calulcateAlternatePredictions.Rd | 110 healthcareai-1.0.0/healthcareai/man/convertDateTimeColToDummies.Rd | 94 healthcareai-1.0.0/healthcareai/man/countDaysSinceFirstDate.Rd | 78 healthcareai-1.0.0/healthcareai/man/countMissingData.Rd |only healthcareai-1.0.0/healthcareai/man/countPercentEmpty.Rd | 62 healthcareai-1.0.0/healthcareai/man/createAllCombinations.Rd |only healthcareai-1.0.0/healthcareai/man/createVarianceTallTable.Rd |only healthcareai-1.0.0/healthcareai/man/dataScale.Rd |only healthcareai-1.0.0/healthcareai/man/distancePointLine.Rd |only healthcareai-1.0.0/healthcareai/man/distancePointSegment.Rd |only healthcareai-1.0.0/healthcareai/man/featureAvailabilityProfiler.Rd | 110 healthcareai-1.0.0/healthcareai/man/findBestAlternateScenarios.Rd | 126 healthcareai-1.0.0/healthcareai/man/findElbow.Rd |only healthcareai-1.0.0/healthcareai/man/findTrends.Rd | 90 healthcareai-1.0.0/healthcareai/man/findVariation.Rd |only healthcareai-1.0.0/healthcareai/man/generateAUC.Rd | 119 healthcareai-1.0.0/healthcareai/man/getCutOffList.Rd | 58 healthcareai-1.0.0/healthcareai/man/getPipedValue.Rd |only healthcareai-1.0.0/healthcareai/man/getPipedWordCount.Rd |only healthcareai-1.0.0/healthcareai/man/groupedLOCF.Rd | 82 healthcareai-1.0.0/healthcareai/man/healthcareai.Rd | 196 healthcareai-1.0.0/healthcareai/man/ignoreSpecWarn.Rd |only healthcareai-1.0.0/healthcareai/man/imputeColumn.Rd | 55 healthcareai-1.0.0/healthcareai/man/imputeDF.Rd |only healthcareai-1.0.0/healthcareai/man/initializeParamsForTesting.Rd | 47 healthcareai-1.0.0/healthcareai/man/isBinary.Rd | 54 healthcareai-1.0.0/healthcareai/man/isNumeric.Rd |only healthcareai-1.0.0/healthcareai/man/isTargetYN.Rd |only healthcareai-1.0.0/healthcareai/man/lineMagnitude.Rd |only healthcareai-1.0.0/healthcareai/man/orderByDate.Rd | 66 healthcareai-1.0.0/healthcareai/man/pcaAnalysis.Rd |only healthcareai-1.0.0/healthcareai/man/percentDataAvailableInDateRange.Rd | 92 healthcareai-1.0.0/healthcareai/man/plotPRCurve.Rd | 48 healthcareai-1.0.0/healthcareai/man/plotProfiler.Rd | 74 healthcareai-1.0.0/healthcareai/man/plotROCs.Rd | 48 healthcareai-1.0.0/healthcareai/man/removeColsWithAllSameValue.Rd | 66 healthcareai-1.0.0/healthcareai/man/removeColsWithDTSSuffix.Rd |only healthcareai-1.0.0/healthcareai/man/removeColsWithOnlyNA.Rd |only healthcareai-1.0.0/healthcareai/man/removeRowsWithNAInSpecCol.Rd | 60 healthcareai-1.0.0/healthcareai/man/returnColsWithMoreThanFiftyCategories.Rd | 72 healthcareai-1.0.0/healthcareai/man/selectData.Rd | 143 healthcareai-1.0.0/healthcareai/man/skip_if_no_MSSQL.Rd |only healthcareai-1.0.0/healthcareai/man/variationAcrossGroups.Rd |only healthcareai-1.0.0/healthcareai/man/writeData.Rd | 184 healthcareai-1.0.0/healthcareai/tests/testthat.R | 8 healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_info_LMM.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_info_RF.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_info_XGB.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_info_lasso.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_info_non-deterministic-tree-ensemble.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_info_non-deterministic-tree-ensemble_RF.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_probability_LMM.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_probability_RF.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_probability_XGB.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_probability_lasso.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_probability_non-deterministic-tree-ensemble.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/rmodel_probability_non-deterministic-tree-ensemble_RF.rda |only healthcareai-1.0.0/healthcareai/tests/testthat/test-XGBoost-deploy-pushes-to-sql.R |only healthcareai-1.0.0/healthcareai/tests/testthat/test-calculate-coefficient-of-variation-COV.R |only healthcareai-1.0.0/healthcareai/tests/testthat/test-calculate-confusion.R |only healthcareai-1.0.0/healthcareai/tests/testthat/test-calculate-hour-bins.R | 22 healthcareai-1.0.0/healthcareai/tests/testthat/test-count-missing-data.R |only healthcareai-1.0.0/healthcareai/tests/testthat/test-count-percent-empty.R | 26 healthcareai-1.0.0/healthcareai/tests/testthat/test-create-variance-tall-table.R |only healthcareai-1.0.0/healthcareai/tests/testthat/test-data-scale.R |only healthcareai-1.0.0/healthcareai/tests/testthat/test-deploy-pushes-to-sql-server.R |only healthcareai-1.0.0/healthcareai/tests/testthat/test-deploy-pushes-to-sqlite.R |only healthcareai-1.0.0/healthcareai/tests/testthat/test-deploy-specific-values.R |only healthcareai-1.0.0/healthcareai/tests/testthat/test-deploy-to-df-has-no-nulls.R |only healthcareai-1.0.0/healthcareai/tests/testthat/test-develop-supervised-model.R | 373 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Title: Optimized Kernel Regularized Least Squares
Description: Functions for Kernel-Regularized Least Squares optimized for speed and memory usage are provided along with visualization tools.
For working papers, sample code, and recent presentations visit <https://sites.google.com/site/petemohanty/software/>. bigKRLS, as well its dependencies, require current versions of R and its compilers (and RStudio if used). For details, see <https://github.com/rdrr1990/code/blob/master/bigKRLS_installation.md>.
Author: Pete Mohanty [aut, cre],
Robert Shaffer [aut]
Maintainer: Pete Mohanty <pete.mohanty@gmail.com>
Diff between bigKRLS versions 1.5.3 dated 2017-06-14 and 2.0.0 dated 2017-09-11
bigKRLS-1.5.3/bigKRLS/README.md |only bigKRLS-1.5.3/bigKRLS/src/bigKRLS_init.c |only bigKRLS-1.5.3/bigKRLS/src/tcrossprod.cpp |only bigKRLS-2.0.0/bigKRLS/DESCRIPTION | 18 bigKRLS-2.0.0/bigKRLS/MD5 | 58 - bigKRLS-2.0.0/bigKRLS/NAMESPACE | 2 bigKRLS-2.0.0/bigKRLS/R/RcppExports.R | 24 bigKRLS-2.0.0/bigKRLS/R/bigKRLS.R | 1035 +++++++++++++++------ bigKRLS-2.0.0/bigKRLS/R/init.R | 4 bigKRLS-2.0.0/bigKRLS/R/utils.R | 4 bigKRLS-2.0.0/bigKRLS/build/vignette.rds |binary bigKRLS-2.0.0/bigKRLS/inst/doc/bigKRLS_basics.R | 20 bigKRLS-2.0.0/bigKRLS/inst/doc/bigKRLS_basics.Rmd | 37 bigKRLS-2.0.0/bigKRLS/inst/doc/bigKRLS_basics.html | 108 +- bigKRLS-2.0.0/bigKRLS/man/bigKRLS.Rd | 21 bigKRLS-2.0.0/bigKRLS/man/crossvalidate.bigKRLS.Rd |only bigKRLS-2.0.0/bigKRLS/man/load.bigKRLS.Rd | 11 bigKRLS-2.0.0/bigKRLS/man/predict.bigKRLS.Rd | 7 bigKRLS-2.0.0/bigKRLS/man/save.bigKRLS.Rd | 9 bigKRLS-2.0.0/bigKRLS/man/summary.bigKRLS.Rd | 12 bigKRLS-2.0.0/bigKRLS/man/summary.bigKRLS_CV.Rd |only bigKRLS-2.0.0/bigKRLS/src/Makevars | 2 bigKRLS-2.0.0/bigKRLS/src/Makevars.win | 2 bigKRLS-2.0.0/bigKRLS/src/Neffective.cpp |only bigKRLS-2.0.0/bigKRLS/src/RcppExports.cpp | 67 - bigKRLS-2.0.0/bigKRLS/src/bigderiv_v2.cpp | 6 bigKRLS-2.0.0/bigKRLS/src/crossprod.cpp | 22 bigKRLS-2.0.0/bigKRLS/src/gauss_kernel.cpp | 19 bigKRLS-2.0.0/bigKRLS/src/multdiag.cpp | 1 bigKRLS-2.0.0/bigKRLS/src/solveforc.cpp | 2 bigKRLS-2.0.0/bigKRLS/src/temp_kernel.cpp | 2 bigKRLS-2.0.0/bigKRLS/tests |only bigKRLS-2.0.0/bigKRLS/vignettes/bigKRLS_basics.Rmd | 37 33 files changed, 1103 insertions(+), 427 deletions(-)
Title: Client for the Cancer Imaging Archive REST API
Description: A wrapper for The Cancer Imaging Archive's REST API. The Cancer
Imaging Archive (TCIA) hosts de-identified medical images of cancer
available for public download, as well as rich metadata for each image
series. TCIA provides a REST API for programmatic access to the data.
This package provides simple functions to access each API endpoint.
For more information, see <https://github.com/pamelarussell/TCIApathfinder>
and TCIA's website.
Author: Pamela Russell [aut, cre]
Maintainer: Pamela Russell <pamela.russell@ucdenver.edu>
Diff between TCIApathfinder versions 1.0.0 dated 2017-08-20 and 1.0.1 dated 2017-09-11
TCIApathfinder-1.0.0/TCIApathfinder/NEWS.md |only TCIApathfinder-1.0.1/TCIApathfinder/DESCRIPTION | 8 +++++--- TCIApathfinder-1.0.1/TCIApathfinder/MD5 | 12 ++++++++++-- TCIApathfinder-1.0.1/TCIApathfinder/build |only TCIApathfinder-1.0.1/TCIApathfinder/inst |only TCIApathfinder-1.0.1/TCIApathfinder/vignettes |only 6 files changed, 15 insertions(+), 5 deletions(-)
More information about TCIApathfinder at CRAN
Permanent link
Title: Font Files for the 'showtext' Package
Description: Providing font files that can be used by the 'showtext' package.
Author: Yixuan Qiu and authors/contributors of the included fonts. See file
AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtextdb versions 1.0 dated 2015-03-10 and 2.0 dated 2017-09-11
showtextdb-1.0/showtextdb/R/load_fonts.R |only showtextdb-1.0/showtextdb/man/load_fonts.Rd |only showtextdb-2.0/showtextdb/DESCRIPTION | 14 ++++++++------ showtextdb-2.0/showtextdb/MD5 | 12 ++++++++---- showtextdb-2.0/showtextdb/NAMESPACE | 5 ++++- showtextdb-2.0/showtextdb/R/font_install.R |only showtextdb-2.0/showtextdb/R/load_showtext_fonts.R |only showtextdb-2.0/showtextdb/R/source_han.R |only showtextdb-2.0/showtextdb/man/font_install.Rd |only showtextdb-2.0/showtextdb/man/load_showtext_fonts.Rd |only showtextdb-2.0/showtextdb/man/source_han.Rd |only 11 files changed, 20 insertions(+), 11 deletions(-)
Title: Generalized Correlations and Initial Causal Path
Description: Since causal paths from data are important for all sciences, the
package provides sophisticated functions. The idea is simply
that if X causes Y (path: X to Y) then non-deterministic variation in X
is more "original or independent" than similar variation in Y. We compare
two flipped kernel regressions: X=f(Y, Z) and Y=g(X,Z), where Z are control
variables. Our first two criteria compare absolute gradients (Cr1) and
absolute residuals (Cr2), both quantified by stochastic dominance of four
orders (SD1 to SD4). Our third criterion (Cr3) expects X to be better able
to predict Y than the other way around using generalized partial correlation
If |r*(x|y)|> |r*(y|x)| it suggests that y is more likely
the "kernel cause" of x. The usual partial correlations are generalized for
the asymmetric matrix of r*'s developed here.
Partial correlations help asses effect of x on y after removing the effect of a
set of variables.
The package provides additional tools for causal assessment,
for printing the causal directions in a clear, comprehensive compact summary form,
for matrix algebra, for "outlier detection", and for numerical integration by the
trapezoidal rule, stochastic dominance, etc.
The package has functions for bootstrap-based statistical inference and one
for a heuristic t-test.
Author: Prof. H. D. Vinod, Fordham University, NY.
Maintainer: H. D. Vinod <vinod@fordham.edu>
Diff between generalCorr versions 1.0.7 dated 2017-09-02 and 1.0.8 dated 2017-09-11
generalCorr-1.0.7/generalCorr/R/parcorSilent.R |only generalCorr-1.0.7/generalCorr/R/parcor_ridg.R |only generalCorr-1.0.7/generalCorr/man/parcorSilent.Rd |only generalCorr-1.0.7/generalCorr/man/parcor_ridg.Rd |only generalCorr-1.0.8/generalCorr/DESCRIPTION | 8 - generalCorr-1.0.8/generalCorr/MD5 | 26 ++-- generalCorr-1.0.8/generalCorr/NAMESPACE | 2 generalCorr-1.0.8/generalCorr/NEWS | 5 generalCorr-1.0.8/generalCorr/R/kern_ctrl.R | 2 generalCorr-1.0.8/generalCorr/R/parcor_ijk.R | 54 +++------- generalCorr-1.0.8/generalCorr/R/silentPairs.R | 7 - generalCorr-1.0.8/generalCorr/R/someCPairs.R | 8 - generalCorr-1.0.8/generalCorr/inst/doc/generalCorr-vignette.pdf |binary generalCorr-1.0.8/generalCorr/inst/doc/generalCorr-vignette2.pdf |binary generalCorr-1.0.8/generalCorr/inst/doc/generalCorr-vignette3.pdf |binary generalCorr-1.0.8/generalCorr/man/parcor_ijk.Rd | 30 ++--- 16 files changed, 56 insertions(+), 86 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-13 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-16 1.0-0
2013-12-11 0.9-5
2009-11-02 0.9-2
2008-01-09 0.9-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-07 1.0-5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-01 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-17 1.3
2014-06-01 1.2
2013-02-24 1.1
2012-04-30 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-29 0.96
2014-09-26 0.95
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-23 3010.79
2013-02-08 3000.78
2012-03-21 2160.77
2009-09-30 2100.76
2009-04-16 290.75
2008-10-27 270.74
2008-10-23 270.73
2007-10-08 260.72
2007-10-02 260.71
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-28 0.0.4
2016-11-24 0.0.3
2016-11-22 0.0.2
2016-07-26 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-23 3010.79
2012-09-17 2160.78
2012-03-20 2160.77
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-13 1.0.8
2015-02-06 1.0.6
2014-03-28 1.0.2
2014-01-30 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-09 0.5
More information about sutteForecastR at CRAN
Permanent link
Title: Subtracting Summary Statistics of One or more Cohorts from
Meta-GWAS Results
Description: If results from a meta-GWAS are used for validation in one of the cohorts that was included in the meta-analysis, this will yield biased (i.e. too optimistic) results. The validation cohort needs to be independent from the meta-GWAS results. MetaSubtract will subtract the results of the respective cohort from the meta-GWAS results analytically without having to redo the meta-GWAS analysis using the leave-one-out methodology. It can handle different meta-analyses methods and takes into account if single or double genomic control correction was applied to the original meta-analysis. It can be used for whole GWAS, but also for a limited set of SNPs or other genetic markers.
Author: Ilja M. Nolte
Maintainer: Ilja M. Nolte <i.m.nolte@umcg.nl>
Diff between MetaSubtract versions 1.0 dated 2017-07-11 and 1.1 dated 2017-09-11
MetaSubtract-1.0/MetaSubtract/build |only MetaSubtract-1.1/MetaSubtract/DESCRIPTION | 8 MetaSubtract-1.1/MetaSubtract/MD5 | 17 MetaSubtract-1.1/MetaSubtract/NAMESPACE | 3 MetaSubtract-1.1/MetaSubtract/R/MetaSubtract.r | 74 MetaSubtract-1.1/MetaSubtract/inst/extdata/alternative_headers.txt | 6 MetaSubtract-1.1/MetaSubtract/inst/extdata/cohort1_results.txt | 996 ++++------ MetaSubtract-1.1/MetaSubtract/inst/extdata/cohort2_results.txt | 859 ++++---- MetaSubtract-1.1/MetaSubtract/man/MetaSubtract-package.Rd | 8 MetaSubtract-1.1/MetaSubtract/man/meta.subtract.Rd | 28 10 files changed, 989 insertions(+), 1010 deletions(-)
Title: Create Muller Plots of Evolutionary Dynamics
Description: Create plots that combine a phylogeny and frequency dynamics.
Phylogenetic input can be a generic adjacency matrix or a tree of class "phylo".
Inspired by similar plots in publications of the labs of RE Lenski and JE
Barrick. Named for HJ Muller (who popularised such plots) and H Wickham (whose
code this package exploits).
Author: Robert Noble [aut, cre]
Maintainer: Robert Noble <robjohnnoble@gmail.com>
Diff between ggmuller versions 0.2.0 dated 2017-09-01 and 0.2.2 dated 2017-09-11
DESCRIPTION | 6 +-- MD5 | 18 +++++------ R/MullerPlot.R | 76 ++++++++++++++++++------------------------------ README.md | 42 +++++++++++++++++++++----- inst/doc/ggmuller.R | 21 ++++++++----- inst/doc/ggmuller.Rmd | 30 ++++++++++-------- inst/doc/ggmuller.html | 42 +++++++++++++------------- man/add_start_points.Rd | 4 +- man/get_Muller_df.Rd | 15 +++------ vignettes/ggmuller.Rmd | 30 ++++++++++-------- 10 files changed, 149 insertions(+), 135 deletions(-)
Title: Do a Git Style Diff of the Rows Between Two Dataframes with
Similar Structure
Description: Compares two dataframes which have the same column
structure to show the rows that have changed. Also gives a git style diff format
to quickly see what has changes in addition to summary statistics.
Author: Alex Joseph [aut, cre]
Maintainer: Alex Joseph <alexsanjoseph@gmail.com>
Diff between compareDF versions 1.1.0 dated 2017-01-18 and 1.2.0 dated 2017-09-11
DESCRIPTION | 10 +++--- MD5 | 17 +++++----- NAMESPACE | 1 NEWS.md | 10 ++++++ R/fnsComparison.R | 43 ++++++++++++++++++++++---- man/compare_df.Rd | 1 man/results_2010.Rd | 1 man/results_2011.Rd | 1 man/view_html.Rd |only tests/testthat/test-fnsComparison.R | 59 ++++++++++++++++++++++++++++++++---- 10 files changed, 116 insertions(+), 27 deletions(-)
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and
writing data between R and other statistical software packages like 'SPSS',
'SAS' or 'Stata', and working with labelled data. This includes easy ways
to get, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.0.1 dated 2017-07-08 and 1.0.2 dated 2017-09-11
DESCRIPTION | 10 - MD5 | 26 +- NAMESPACE | 1 NEWS | 36 ++- NEWS.md | 46 ++-- R/get_label.R | 21 +- R/get_model_labels.R | 262 +++++++++++++++------------ R/helpfunctions.R | 350 +++++++++++++++++++----------------- R/to_value.R | 394 ++++++++++++++++++++--------------------- README.md | 68 +++---- inst/doc/intro_sjlabelled.html | 130 ++++++------- inst/doc/labelleddata.html | 20 +- man/get_label.Rd | 11 + man/get_term_labels.Rd | 18 + 14 files changed, 742 insertions(+), 651 deletions(-)
Title: Latent Trait Models under IRT
Description: Analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded Response, and the Generalized Partial Credit Models.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between ltm versions 1.0-0 dated 2013-12-20 and 1.1-0 dated 2017-09-11
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 21 +++++++++++++++++++-- R/fscores.l.R | 6 +++--- R/fscores.t.R | 2 +- R/globals.R | 5 +++-- inst/NEWS | 8 ++++++++ man/WIRS.Rd | 3 --- man/ltm-package.Rd | 6 ++---- 9 files changed, 49 insertions(+), 28 deletions(-)
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 2.1.5 dated 2017-07-31 and 2.1.6 dated 2017-09-11
DESCRIPTION | 8 MD5 | 22 NAMESPACE | 2 R/gjamHfunctions.R | 994 +++++++++------ inst/doc/gjamVignette.R | 61 inst/doc/gjamVignette.Rmd | 91 + inst/doc/gjamVignette.html | 2823 +++++++++++++++++++-------------------------- man/gjam-package.Rd | 4 man/gjamPlot.Rd | 226 +-- man/gjamPredict.Rd | 7 man/gjamPriorTemplate.Rd | 6 vignettes/gjamVignette.Rmd | 91 + 12 files changed, 2191 insertions(+), 2144 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions and
Transport Formulas in Causal Models
Description: Functions for identification and transportation of causal effects. Provides a conditional causal effect identification algorithm (IDC) by Shpitser, I. and Pearl, J. (2006) <http://ftp.cs.ucla.edu/pub/stat_ser/r329-uai.pdf>, an algorithm for transportability from multiple domains with limited experiments by Bareinboim, E. and Pearl, J. (2014) <http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf> and a selection bias recovery algorithm by Bareinboim, E. and Tian, J. (2015) <http://ftp.cs.ucla.edu/pub/stat_ser/r445.pdf>. All of the previously mentioned algorithms are based on a causal effect identification algorithm by Tian , J. (2002) <http://ftp.cs.ucla.edu/pub/stat_ser/r309.pdf>.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between causaleffect versions 1.3.4 dated 2017-05-10 and 1.3.5 dated 2017-09-11
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++++------------------ NAMESPACE | 3 ++- NEWS | 3 +++ R/ancestors.R | 6 +++--- R/causal.effect.R | 7 ++++--- R/children.R |only R/compare.graphs.R |only R/connected.R | 6 +++--- R/descendants.R | 6 +++--- R/id.R | 14 ++++---------- R/idc.R | 7 ++++--- R/latent.projection.R |only R/pid.R |only R/trmz.R | 4 +++- inst/doc/causaleffect.pdf |binary inst/doc/simplification.pdf |binary man/causal.effect.Rd | 21 ++++++++++++++------- man/generalize.Rd | 2 +- man/meta.transport.Rd | 2 +- man/recover.Rd | 2 +- man/transport.Rd | 2 +- man/zzaux.effect.Rd | 2 +- 23 files changed, 74 insertions(+), 61 deletions(-)
Title: Read Windows Bitmap (BMP) Images
Description: Reads Windows BMP format images. Currently limited to 8 bit
greyscale images and 24,32 bit (A)RGB images. Pure R implementation without
external dependencies.
Author: Gregory Jefferis
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between bmp versions 0.2 dated 2013-08-09 and 0.3 dated 2017-09-11
bmp-0.2/bmp/inst/tests |only bmp-0.3/bmp/DESCRIPTION | 10 +++++----- bmp-0.3/bmp/MD5 | 24 ++++++++++++------------ bmp-0.3/bmp/NAMESPACE | 2 ++ bmp-0.3/bmp/R/read-bmp.R | 8 +++++--- bmp-0.3/bmp/README.md | 7 +++++-- bmp-0.3/bmp/man/ConvertIntToUInt.Rd | 23 +++++++++++------------ bmp-0.3/bmp/man/is.bmp.Rd | 14 +++++++------- bmp-0.3/bmp/man/read.bmp.Rd | 17 +++++++++-------- bmp-0.3/bmp/tests/test-all.R | 2 +- bmp-0.3/bmp/tests/testthat |only 11 files changed, 57 insertions(+), 50 deletions(-)
Title: Compute Node Overlap and Segregation in Ecological Networks
Description: Calculate NOS (node overlap and segregation) and
the associated metrics described in Strona and Veech (2015)
<DOI:10.1111/2041-210X.12395> and Strona et al. (2017, In Press).
The functions provided in the package enable assessment of
structural patterns ranging from complete node segregation to perfect
nestedness in a variety of network types. In addition, they provide a
measure of network modularity.
Author: Thomas J. Matthews and Giovanni Strona
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Diff between nos versions 1.0.0 dated 2017-05-31 and 1.1.0 dated 2017-09-11
DESCRIPTION | 19 +++++++++---------- MD5 | 35 +++++++++++++++++++---------------- NAMESPACE | 1 + NEWS.md |only R/bip.R | 5 ++++- R/dir.R | 5 ++++- R/int_fun.R | 1 + R/int_fun2.R | 3 +++ R/mat_2_edge.R |only R/nos.R | 7 +++++++ R/pot_dir.R | 5 ++++- R/pot_undir.R | 5 ++++- R/undir.R | 5 ++++- man/NOSM_POT_dir.Rd | 5 ++++- man/NOSM_POT_undir.Rd | 5 ++++- man/NOSM_bip.Rd | 5 ++++- man/NOSM_dir.Rd | 5 ++++- man/NOSM_undir.Rd | 5 ++++- man/freqMat_2_edge.Rd |only man/nos-package.Rd | 7 +++++++ 20 files changed, 87 insertions(+), 36 deletions(-)
Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Baltagi (2011) <doi:10.1007/978-3-642-20059-5> for more information.
Author: Haydar Demirhan
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>
Diff between dLagM versions 0.0.9 dated 2017-09-04 and 0.1.0 dated 2017-09-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/MASE.default.R | 24 ++++++++++++++++++++---- R/ardlDlm.main.R | 6 +++--- R/koyckDlm.main.R | 4 ++-- man/MASE.Rd | 33 +++++++++++++++++++++++++++++---- man/dLagM-package.Rd | 4 ++-- 7 files changed, 66 insertions(+), 25 deletions(-)
Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas, data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data).
(MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>,
HUBERT, L., ARABIE, P. (1985), <doi:10.1007%2FBF01908075>,
RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>,
JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>,
MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>,
CORMACK, R.M. (1971) <doi:10.2307/2344237>,
JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>,
CARMONE, F.J., KARA, A., MAXWELL, S. (1999) <doi:10.2307/3152003>,
DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>,
CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>,
HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>,
TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>,
KRZANOWSKI, W.J., LAI, Y.T. (1988) <doi:10.2307/2531893>,
BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>,
WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl> Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between clusterSim versions 0.45-2 dated 2017-03-31 and 0.46-1 dated 2017-09-11
DESCRIPTION | 25 +++- MD5 | 57 ++++----- R/data.Normalization.r | 220 ++++++++++++++++++++++++++++++++++-- R/pattern.GDM2.r | 2 man/HINoV.Mod.rd | 8 - man/HINoV.Symbolic.rd | 8 - man/cluster.Gen.rd | 26 ++-- man/cluster.Sim.rd | 14 +- man/comparing.Partitions.rd | 5 man/data.Normalization.rd | 13 +- man/dist.BC.rd | 4 man/dist.GDM.rd | 7 - man/dist.SM.rd | 4 man/dist.Symbolic.rd | 2 man/index.DB.rd | 3 man/index.G1.rd | 11 - man/index.G2.rd | 11 - man/index.G3.rd | 7 - man/index.GAP.rd | 3 man/index.H.rd | 7 - man/index.KL.rd | 6 man/index.S.rd | 4 man/initial.Centers.rd | 2 man/ordinalToMetric.rd | 10 - man/pattern.GDM1.rd | 10 - man/pattern.GDM2.rd | 12 + man/replication.Mod.rd | 12 - man/speccl.rd | 10 + src/clusterSim.cpp | 5 tests/testthat/test_normalization.R |only 30 files changed, 367 insertions(+), 141 deletions(-)
Title: The Serial Interface Package
Description: Provides functionality for the use of the internal hardware for
RS232/RS422/RS485 and any other virtual serial interfaces of the
computer.
Author: Martin Seilmayer
Maintainer: Martin Seilmayer <m.seilmayer@hzdr.de>
Diff between serial versions 1.2 dated 2016-04-11 and 1.3 dated 2017-09-11
DESCRIPTION | 8 +- MD5 | 28 ++++---- NAMESPACE | 24 +++--- R/init.R | 109 ++++++++++++++++++------------- R/serial.R | 28 ++++---- man/close.serialConnection.Rd | 40 +++++------ man/isOpen.Rd | 34 ++++----- man/isOpen.default.Rd | 40 +++++------ man/isOpen.serialConnection.Rd | 40 +++++------ man/listPorts.Rd | 98 ++++++++++++++-------------- man/open.serialConnection.Rd | 40 +++++------ man/read.serialConnection.Rd | 50 +++++++------- man/serial.Rd | 142 ++++++++++++++++++++--------------------- man/serialConnection.Rd | 28 +++++--- man/write.serialConnection.Rd | 52 +++++++-------- 15 files changed, 395 insertions(+), 366 deletions(-)
Title: Gaussian Process Fitting
Description: Fits a Gaussian process model to data. Gaussian processes
are commonly used in computer experiments to fit an interpolating model.
The model is stored as an 'R6' object and can be easily updated with new
data. There are options to run in parallel (not for Windows), and 'Rcpp'
has been used to speed up calculations. Other R packages that perform
similar calculations include 'laGP', 'DiceKriging', 'GPfit', and 'mlegp'.
Author: Collin Erickson
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between GauPro versions 0.2.1 dated 2017-09-08 and 0.2.2 dated 2017-09-11
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ R/GauPro_Gauss.R | 2 +- R/GauPro_base.R | 4 ++-- R/kernel_model.R | 4 ++-- inst/doc/CrossValidationErrorCorrection.html | 20 ++++++++++---------- inst/doc/GauPro.html | 4 ++-- inst/doc/IntroductionToGPs.html | 4 ++-- inst/doc/derivatives.html | 4 ++-- inst/doc/surface_derivatives.html | 4 ++-- src/Gaussian_hessian.cpp | 18 +++++++++++++----- 12 files changed, 54 insertions(+), 42 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions. Implementations of
DTW barycenter averaging and a distance based on global alignment kernels
are also provided. All included distance functions have custom loops
optimized for the calculation of cross-distance matrices, including
parallelization support. Several cluster validity indices are included.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 4.0.3 dated 2017-08-09 and 4.1.0 dated 2017-09-11
DESCRIPTION | 8 MD5 | 157 - NAMESPACE | 4 R/DBA.R | 299 +-- R/Distmat.R | 192 +- R/GAK.R | 703 +++---- R/NCCc.R | 52 R/SBD.R | 5 R/SparseDistmat.R | 211 +- R/TADPole.R | 223 +- R/compare-clusterings.R | 32 R/compute-envelope.R | 116 - R/create-dtwclust.R | 267 +- R/cvi.R | 68 R/data.R | 98 - R/dtw-basic.R | 506 ++--- R/dtw-lb.R | 562 +++--- R/dtw2.R | 107 - R/dtwclust-classes.R | 401 ++-- R/dtwclust-methods.R | 1709 +++++++++--------- R/dtwclust.R | 1249 ++++++------- R/partitional.R | 46 R/pkg.R | 6 R/shape-extraction.R | 226 +- R/tsclust-classes.R | 2 R/tsclust-controls.R | 46 R/tsclust-family.R | 247 +- R/tsclust-methods.R | 181 +- R/tsclust.R | 1484 ++++++++-------- R/tslist.R | 80 R/zscore.R | 2 inst/NEWS.Rd | 33 inst/doc/dtwclust.Rnw | 3513 +++++++++++++++++++-------------------- inst/doc/dtwclust.pdf |binary inst/doc/timing-experiments.R |only inst/doc/timing-experiments.Rmd | 32 inst/doc/timing-experiments.html | 50 man/DBA.Rd | 9 man/Distmat-class.Rd | 4 man/Distmat-generics.Rd | 1 man/GAK.Rd | 4 man/NCCc.Rd | 4 man/SBD.Rd | 3 man/SparseDistmat-class.Rd | 5 man/SparseDistmat-generics.Rd | 1 man/TADPole.Rd | 12 man/TSClusters-class.Rd | 2 man/clusterSim.Rd | 1 man/compare_clusterings.Rd | 57 man/compute_envelope.Rd | 2 man/create_dtwclust.Rd | 1 man/cvi.Rd | 89 man/dtw2.Rd | 3 man/dtw_basic.Rd | 4 man/dtw_lb.Rd | 2 man/dtwclust-class.Rd | 1 man/dtwclust-methods.Rd | 1 man/dtwclust-package.Rd | 6 man/dtwclust.Rd | 1 man/dtwclustControl-class.Rd | 1 man/dtwclustFamily-class.Rd | 1 man/dtwclustTimings.Rd | 2 man/pdc_configs.Rd | 15 man/randIndex.Rd | 1 man/shape_extraction.Rd | 2 man/tsclust-controls.Rd | 23 man/tsclust.Rd | 45 man/tsclustFamily-class.Rd | 5 man/tsclusters-methods.Rd | 48 man/tslist.Rd | 2 man/uciCT.Rd | 2 src/dba.cpp | 12 src/tadpole.cpp | 13 tests/testthat/helper-all.R | 2 tests/testthat/regression/cvis.R | 1 tests/testthat/unit/cvis.R | 286 +-- tests/testthat/unit/methods.R | 390 ++-- vignettes/REFERENCES.bib | 11 vignettes/dtwclust.Rnw | 3513 +++++++++++++++++++-------------------- vignettes/timing-experiments.Rmd | 32 80 files changed, 8967 insertions(+), 8570 deletions(-)
Title: Data and Methods Around Reference Values in Pediatrics
Description: Calculation of standard deviation scores adduced from different
growth standards (WHO, UK, Germany, Italy, China, etc). Therefore, the calculation of SDS-values
for different measures like BMI, weight, height, head circumference, different
ratios, etc. are easy to carry out. Also, references for laboratory values in
children are available: serum lipids, iron-related blood parameters. In the
new version, there are also functions combining the lms() function from package 'gamlss' with
resampling methods for using with repeated measurements and family dependencies. A searchable list
of items can be found here: <https://github.com/mvogel78/childsds/wiki>.
Author: Mandy Vogel [aut, cre]
Maintainer: Mandy Vogel <mandy.vogel@googlemail.com>
Diff between childsds versions 0.6.5 dated 2017-08-15 and 0.6.6 dated 2017-09-11
DESCRIPTION | 10 +++--- MD5 | 23 ++++++++------ NAMESPACE | 1 NEWS.md | 6 +++ R/createlms.R | 72 ++++++++++++++++++++++++++------------------- R/misc.R | 66 ++++++++++++++++++++++++++++++++++++++--- R/sdsvals.r | 2 - R/zzz.R |only man/do_iterations.Rd | 6 +++ man/fit_gamlss.Rd |only man/make_percentile_tab.Rd | 6 +++ man/one_iteration.Rd | 7 +++- man/sds.Rd | 2 - man/wormplot_gg.Rd |only 14 files changed, 147 insertions(+), 54 deletions(-)
Title: CCDr Algorithm for Learning Sparse Gaussian Bayesian Networks
Description: Implementation of the CCDr (Concave penalized Coordinate Descent with reparametrization) structure learning algorithm as described in Aragam and Zhou (2015) <http://www.jmlr.org/papers/v16/aragam15a.html>. This is a fast, score-based method for learning Bayesian networks that uses sparse regularization and block-cyclic coordinate descent.
Author: Bryon Aragam [aut, cre],
Dacheng Zhang [aut]
Maintainer: Bryon Aragam <sparsebn@gmail.com>
Diff between ccdrAlgorithm versions 0.0.3 dated 2017-03-12 and 0.0.4 dated 2017-09-11
DESCRIPTION | 10 +- MD5 | 38 ++++---- NEWS.md | 11 ++ R/RcppExports.R | 8 - R/ccdrAlgorithm-bwlist.R |only R/ccdrAlgorithm-main.R | 116 +++++++++++++++++++++--- R/ccdrAlgorithm-mvn.R | 39 ++++++++ README.md | 16 +-- man/ccdr.run.Rd | 31 +++++- man/generate_mvn_data.Rd | 21 ++++ src/CCDrAlgorithm.h | 132 ++++++++++++++++++++-------- src/CCDrAlgorithm_old.h |only src/RcppExports.cpp | 27 ++++- src/algorithm.h | 140 ++++++++++++++++++++---------- src/rcpp_wrap.cpp | 16 ++- tests/testthat/test-bwlist.R |only tests/testthat/test-ccdr_call.R | 39 +++++--- tests/testthat/test-ccdr_gridR.R | 5 - tests/testthat/test-ccdr_singleR.R | 172 +++++++++++++++++++++++++++++-------- tests/testthat/test-mvn.R | 14 +++ tests/testthat/test-sigmas.R |only tests/testthat/test-test_cases.R | 4 22 files changed, 637 insertions(+), 202 deletions(-)
Title: A Shiny GUI for Smith's Mean Measure of Divergence (MMD)
Description: Offers a Shiny user interface for the calculation of the Mean Measure of Divergence, with facilities for trait selection and graphical representations.
Author: Frederic Santos
Maintainer: Frederic Santos <frederic.santos@u-bordeaux.fr>
Diff between AnthropMMD versions 2.2.0 dated 2017-08-16 and 2.2.1 dated 2017-09-11
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ inst/AnthropMMDShinyApp/calcMMD.R | 8 ++++---- inst/AnthropMMDShinyApp/server.R | 4 ++-- inst/AnthropMMDShinyApp/ui.R | 7 +++++-- inst/CITATION |only man/AnthropMMD-package.Rd | 8 ++++---- man/StartMMD.Rd | 6 +++--- 8 files changed, 30 insertions(+), 26 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Sydney E. Everhart [ctb, dtc],
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb],
Erik Sotka [ctb],
Brian J. Knaus [ctb],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between poppr versions 2.4.1 dated 2017-04-14 and 2.5.0 dated 2017-09-11
poppr-2.4.1/poppr/R/sandbox.r |only poppr-2.4.1/poppr/man/jack.ia.Rd |only poppr-2.5.0/poppr/DESCRIPTION | 12 poppr-2.5.0/poppr/MD5 | 73 ++--- poppr-2.5.0/poppr/NAMESPACE | 4 poppr-2.5.0/poppr/NEWS | 49 +++ poppr-2.5.0/poppr/R/Index_calculations.r | 39 ++ poppr-2.5.0/poppr/R/bootstraping.R | 31 -- poppr-2.5.0/poppr/R/bruvo.r | 54 ++- poppr-2.5.0/poppr/R/file_handling.r | 83 +++-- poppr-2.5.0/poppr/R/ia_jackknife.R | 35 +- poppr-2.5.0/poppr/R/internal.r | 224 ++++++++------- poppr-2.5.0/poppr/R/messages.r | 13 poppr-2.5.0/poppr/R/methods.r | 13 poppr-2.5.0/poppr/R/round_robin.R | 4 poppr-2.5.0/poppr/R/visualizations.r | 83 ++++- poppr-2.5.0/poppr/R/zzz.r | 4 poppr-2.5.0/poppr/build/vignette.rds |binary poppr-2.5.0/poppr/inst/doc/algo.Rnw | 18 - poppr-2.5.0/poppr/inst/doc/algo.pdf |binary poppr-2.5.0/poppr/inst/doc/mlg.html | 72 ++-- poppr-2.5.0/poppr/inst/doc/poppr_manual.html | 92 +++--- poppr-2.5.0/poppr/man/bruvo.dist.Rd | 53 ++- poppr-2.5.0/poppr/man/ia.Rd | 52 +++ poppr-2.5.0/poppr/man/poppr.plot.Rd |only poppr-2.5.0/poppr/man/snpclone-coercion-methods.Rd | 11 poppr-2.5.0/poppr/src/bitwise_distance.c | 2 poppr-2.5.0/poppr/src/init.c | 4 poppr-2.5.0/poppr/src/poppr_distance.c | 290 +++++++++++++++----- poppr-2.5.0/poppr/tests/testthat/test-amova.R | 3 poppr-2.5.0/poppr/tests/testthat/test-filter.R | 3 poppr-2.5.0/poppr/tests/testthat/test-import.R | 25 + poppr-2.5.0/poppr/tests/testthat/test-jackia.R | 20 - poppr-2.5.0/poppr/tests/testthat/test-mlg.R | 22 - poppr-2.5.0/poppr/tests/testthat/test-plots.R | 12 poppr-2.5.0/poppr/tests/testthat/test-round-robin.R | 4 poppr-2.5.0/poppr/tests/testthat/test-trees.R | 17 - poppr-2.5.0/poppr/tests/testthat/test-values.R | 30 +- poppr-2.5.0/poppr/vignettes/algo.Rnw | 18 - 39 files changed, 957 insertions(+), 512 deletions(-)
Title: A Future API for Parallel and Distributed Processing using
'batchtools'
Description: Implementation of the Future API on top of the 'batchtools' package.
This allows you to process futures, as defined by the 'future' package,
in parallel out of the box, not only on your local machine or ad-hoc
cluster of machines, but also via high-performance compute ('HPC') job
schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS',
e.g. 'y <- future_lapply(files, FUN = process)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.batchtools versions 0.5.0 dated 2017-06-03 and 0.6.0 dated 2017-09-11
future.batchtools-0.5.0/future.batchtools/R/batchtoolsFutureError.R |only future.batchtools-0.6.0/future.batchtools/DESCRIPTION | 12 +- future.batchtools-0.6.0/future.batchtools/MD5 | 45 ++++----- future.batchtools-0.6.0/future.batchtools/NAMESPACE | 2 future.batchtools-0.6.0/future.batchtools/NEWS | 37 +++++++ future.batchtools-0.6.0/future.batchtools/R/BatchtoolsFuture-class.R | 48 +++++++--- future.batchtools-0.6.0/future.batchtools/R/BatchtoolsFutureError.R |only future.batchtools-0.6.0/future.batchtools/R/batchtools_custom.R | 2 future.batchtools-0.6.0/future.batchtools/R/batchtools_interactive.R | 2 future.batchtools-0.6.0/future.batchtools/R/batchtools_local.R | 2 future.batchtools-0.6.0/future.batchtools/R/batchtools_multicore.R | 2 future.batchtools-0.6.0/future.batchtools/R/batchtools_template.R | 38 +++++-- future.batchtools-0.6.0/future.batchtools/R/utils.R | 13 ++ future.batchtools-0.6.0/future.batchtools/build/vignette.rds |binary future.batchtools-0.6.0/future.batchtools/inst/templates |only future.batchtools-0.6.0/future.batchtools/man/BatchtoolsFuture.Rd | 4 future.batchtools-0.6.0/future.batchtools/man/BatchtoolsFutureError.Rd | 2 future.batchtools-0.6.0/future.batchtools/man/await.BatchtoolsFuture.Rd | 6 + future.batchtools-0.6.0/future.batchtools/man/batchtools_custom.Rd | 4 future.batchtools-0.6.0/future.batchtools/man/batchtools_local.Rd | 2 future.batchtools-0.6.0/future.batchtools/man/batchtools_multicore.Rd | 4 future.batchtools-0.6.0/future.batchtools/man/batchtools_template.Rd | 20 ++-- future.batchtools-0.6.0/future.batchtools/tests/BatchtoolsFutureError.R | 18 +++ future.batchtools-0.6.0/future.batchtools/tests/future,labels.R | 2 future.batchtools-0.6.0/future.batchtools/tests/future_lapply.R | 12 ++ 25 files changed, 199 insertions(+), 78 deletions(-)
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Title: A Future API for Parallel and Distributed Processing using
BatchJobs
Description: Implementation of the Future API on top of the 'BatchJobs' package.
This allows you to process futures, as defined by the 'future' package,
in parallel out of the box, not only on your local machine or ad-hoc
cluster of machines, but also via high-performance compute ('HPC') job
schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS',
e.g. 'y <- future_lapply(files, FUN = process)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.BatchJobs versions 0.14.1 dated 2017-05-31 and 0.15.0 dated 2017-09-11
future.BatchJobs-0.14.1/future.BatchJobs/R/DEPRECATED.backend.R |only future.BatchJobs-0.14.1/future.BatchJobs/R/DEPRECATED.batchjobs.R |only future.BatchJobs-0.14.1/future.BatchJobs/man/backend.Rd |only future.BatchJobs-0.14.1/future.BatchJobs/man/batchjobs.Rd |only future.BatchJobs-0.14.1/future.BatchJobs/tests/DEPRECATED.backend.R |only future.BatchJobs-0.15.0/future.BatchJobs/DESCRIPTION | 10 +- future.BatchJobs-0.15.0/future.BatchJobs/MD5 | 28 ++--- future.BatchJobs-0.15.0/future.BatchJobs/NAMESPACE | 3 future.BatchJobs-0.15.0/future.BatchJobs/NEWS | 29 ++++++ future.BatchJobs-0.15.0/future.BatchJobs/R/BatchJobsFuture-class.R | 48 +++++----- future.BatchJobs-0.15.0/future.BatchJobs/R/makeBatchJobsConf.R |only future.BatchJobs-0.15.0/future.BatchJobs/build/vignette.rds |binary future.BatchJobs-0.15.0/future.BatchJobs/inst/doc/future.BatchJobs.html | 2 future.BatchJobs-0.15.0/future.BatchJobs/inst/doc/future.BatchJobs.md.rsp | 7 - future.BatchJobs-0.15.0/future.BatchJobs/man/BatchJobsFuture.Rd | 2 future.BatchJobs-0.15.0/future.BatchJobs/tests/BatchJobsFutureError.R | 18 +++ future.BatchJobs-0.15.0/future.BatchJobs/tests/future_lapply.R | 13 ++ future.BatchJobs-0.15.0/future.BatchJobs/vignettes/future.BatchJobs.md.rsp | 7 - 18 files changed, 106 insertions(+), 61 deletions(-)
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