Title: R Interface to WinEdt
Description: A plug in for using WinEdt as an editor for R.
Author: Uwe Ligges <Uwe.Ligges@R-project.org>
with contributions (the original R-Sweave mode) from Gilbert Ritschard and Karl Koeller
Maintainer: Uwe Ligges <Uwe.Ligges@R-project.org>
Diff between RWinEdt versions 2.0-3 dated 2015-05-31 and 2.0-4 dated 2015-06-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/zzz.R | 2 +- inst/doc/RWinEdt.pdf |binary src/Makevars.win | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: Genomic Breeding Tools: Genetic Variance Prediction and
Cross-Validation
Description: The main attribute of 'PopVar' is the prediction of genetic variance in bi-parental populations, from which the package derives its name. 'PopVar' contains a set of functions that use phenotypic and genotypic data from a set of candidate parents to 1) predict the mean, genetic variance, and superior progeny value of all, or a defined set of pairwise bi-parental crosses, and 2) perform cross-validation to estimate genome-wide prediction accuracy of multiple statistical models. More details are available in Mohammadi, Tiede, and Smith (2015). Crop Sci. doi:10.2135/cropsci2015.01.0030. A dataset 'think_barley.rda' is included for reference and examples.
Author: Tyler Tiede [aut, cre], Mohsen Mohammadi [ctb], Kevin P. Smith [ctb]
Maintainer: Tyler Tiede <tyler.tiede7@gmail.com>
Diff between PopVar versions 1.1 dated 2015-04-28 and 1.2 dated 2015-06-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/Internal_PopVar_functions_4.28.15.R | 7 ++----- R/pop.predict_function_4.28.15.R | 34 ++++++++++++++++++++++++---------- R/x.val_function_4.28.15.R | 32 ++++++++++++++++++++++---------- man/pop.predict.Rd | 11 +++++++++-- man/x.val.Rd | 11 +++++++++-- 7 files changed, 76 insertions(+), 39 deletions(-)
Title: Efficient Constrained Based Modelling in R
Description: This Systems Biology Library for R implements algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). Most of the current LP/MILP solvers are supported via additional packages.
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut],
Rajen Piernikarczyk [ctb],
Marc Andre Daxer [ctb],
Benjamin Braasch [ctb],
Abdelmoneim Desouki [ctb],
Martin J. Lercher [ctb]
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between sybil versions 1.2.6 dated 2014-06-04 and 1.3.0 dated 2015-06-17
DESCRIPTION | 25 +- LICENSE |only MD5 | 294 +++++++++++++++++----------------- R/addReact.R | 39 +++- R/doubleFluxDel.R | 50 +++-- R/findExchReact.R | 18 +- R/geneDel.R | 15 + R/generics.R | 2 R/getsybilenv.R | 4 R/modelorgClass.R | 52 +++++- R/multiDel.R | 9 - R/optimizer.R | 12 + R/parseBoolean.R | 19 -- R/rmReact.R | 12 + R/sysBiolAlgClass.R | 35 ++-- R/sysBiolAlg_roomClass.R | 32 ++- README.md |only build/vignette.rds |binary inst/NEWS.Rd | 49 +++++ inst/doc/sybil.R | 168 +++++++++---------- inst/doc/sybil.Rnw | 4 inst/doc/sybil.pdf |binary man/SYBIL_SETTINGS.Rd | 5 man/addAlgorithm.Rd | 5 man/addCols-methods.Rd | 5 man/addColsToProb-methods.Rd | 5 man/addExchReact.Rd | 7 man/addReact.Rd | 19 ++ man/addRows-methods.Rd | 5 man/addRowsCols-methods.Rd | 5 man/addRowsToProb-methods.Rd | 5 man/addSolver.Rd | 7 man/applyChanges-methods.Rd | 17 + man/backupProb-methods.Rd | 5 man/blockedReact.Rd | 5 man/changeBounds.Rd | 7 man/changeColsBnds-methods.Rd | 5 man/changeColsBndsObjCoefs-methods.Rd | 5 man/changeGPR.Rd | 7 man/changeMatrixRow-methods.Rd | 5 man/changeObjCoefs-methods.Rd | 5 man/changeObjFunc.Rd | 7 man/changeRowsBnds-methods.Rd | 5 man/changeUptake-methods.Rd | 5 man/checkAkgorithm.Rd | 5 man/checkDefaultMethod.Rd | 5 man/checkOptSol-methods.Rd | 7 man/checkReactId.Rd | 7 man/checksol-class.Rd | 7 man/deadEndMetabolites-methods.Rd | 5 man/delProb-methods.Rd | 5 man/deprecated.Rd | 5 man/doubleFluxDel.Rd | 7 man/doubleGeneDel.Rd | 7 man/doubleReact.Rd | 7 man/editEnvir.Rd | 7 man/findExchReact.Rd | 7 man/fluxDistribution-class.Rd | 7 man/fluxVar.Rd | 7 man/geneDel.Rd | 5 man/geneDeletion.Rd | 7 man/getColPrim-methods.Rd | 5 man/getColsLowBnds-methods.Rd | 5 man/getColsNames-methods.Rd | 5 man/getColsUppBnds-methods.Rd | 5 man/getFluxDist-methods.Rd | 5 man/getNumCols-methods.Rd | 5 man/getNumNnz-methods.Rd | 5 man/getNumRows-methods.Rd | 5 man/getObjCoefs-methods.Rd | 5 man/getObjDir-methods.Rd | 5 man/getObjVal-methods.Rd | 5 man/getRedCosts-methods.Rd | 5 man/getRowsLowBnds-methods.Rd | 5 man/getRowsNames-methods.Rd | 5 man/getRowsUppBnds-methods.Rd | 5 man/getSolStat-methods.Rd | 5 man/getSolverParm-methods.Rd | 5 man/getsybilenv.Rd | 7 man/initProb-methods.Rd | 5 man/loadLPprob-methods.Rd | 5 man/loadQobj-methods.Rd | 5 man/makeOptsolMO.Rd | 7 man/mod2irrev.Rd | 7 man/modelorg-class.Rd | 18 +- man/modelorg2ExPA.Rd | 5 man/modelorg2tsv.Rd | 5 man/modelorg_irrev-class.Rd | 7 man/multiDel.Rd | 5 man/netFlux-class.Rd | 7 man/oneFluxDel.Rd | 7 man/oneGeneDel.Rd | 7 man/onlyChangeGPR.Rd | 7 man/onlyCheckGPR.Rd | 7 man/optObj-class.Rd | 7 man/optObj.Rd | 5 man/optObj_clpAPI-class.Rd | 7 man/optObj_cplexAPI-class.Rd | 7 man/optObj_glpkAPI-class.Rd | 7 man/optObj_lpSolveAPI-class.Rd | 7 man/optimizeProb-methods.Rd | 23 ++ man/optimizer.Rd | 7 man/optsol-class.Rd | 7 man/optsol_blockedReact-class.Rd | 7 man/optsol_fluxVar-class.Rd | 7 man/optsol_fluxdel-class.Rd | 7 man/optsol_genedel-class.Rd | 10 - man/optsol_optimizeProb-class.Rd | 7 man/optsol_phpp-class.Rd | 7 man/optsol_robAna-class.Rd | 7 man/phpp.Rd | 7 man/ppProc-class.Rd | 7 man/printMetabolite-methods.Rd | 5 man/printReaction-methods.Rd | 5 man/promptSysBiolAlg.Rd | 5 man/reactId-class.Rd | 7 man/reactId_Exch-class.Rd | 21 +- man/readProb-methods.Rd | 32 +++ man/readTSVmod.Rd | 5 man/resetChanges-methods.Rd | 5 man/rmReact.Rd | 7 man/robAna.Rd | 7 man/scaleProb-methods.Rd | 5 man/sensitivityAnalysis-methods.Rd | 5 man/setColsNames-methods.Rd | 5 man/setObjDir-methods.Rd | 5 man/setRhsZero-methods.Rd | 5 man/setRowsNames-methods.Rd | 5 man/setSolverParm-methods.Rd | 5 man/shrinkMatrix-methods.Rd | 5 man/singletonMetabolites-methods.Rd | 5 man/solveLp-methods.Rd | 5 man/summaryOptsol-class.Rd | 5 man/summaryOptsol.Rd | 5 man/sybil-package.Rd | 9 - man/sybilError-class.Rd | 7 man/sybilLog-class.Rd | 7 man/sybilStack.Rd | 5 man/sysBiolAlg-class.Rd | 5 man/sysBiolAlg.Rd | 5 man/sysBiolAlg_fba-class.Rd | 5 man/sysBiolAlg_fv-class.Rd | 5 man/sysBiolAlg_lmoma-class.Rd | 5 man/sysBiolAlg_moma-class.Rd | 5 man/sysBiolAlg_mtf-class.Rd | 5 man/sysBiolAlg_room-class.Rd | 5 man/writeProb-methods.Rd | 31 +++ man/ypd.Rd | 5 vignettes/sybil.Rnw | 4 149 files changed, 1221 insertions(+), 477 deletions(-)
Title: Phylogenetic Comparative Methods for Function-Valued and Other
High-Dimensional Traits
Description: Tools for studying the evolution of function-valued traits (as well as other high-dimensional traits) including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution. Visit http://www.phylocurve.org for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between phylocurve versions 1.2.0 dated 2015-06-13 and 1.3.0 dated 2015-06-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/phylocurve.R | 38 ++++++++++++++++++++++++++++++-------- man/phylocurve-package.Rd | 4 ++-- 4 files changed, 39 insertions(+), 17 deletions(-)
Title: Single-Sample Classifier of Medulloblastoma Subtypes for
Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Description: Description: A single-sample classifier that generates Medulloblastoma (MB) subtype predictions for single-samples of human MB patients and model systems, including cell lines and mouse-models. The MM2S algorithm uses a systems-based methodology that facilitates application of the algorithm on samples irrespective of their platform or source of origin. MM2S demonstrates > 96% accuracy for patients of well-characterized normal cerebellum, Wingless (WNT), or Sonic hedgehog (SHH) subtypes, and the less-characterized Group4 (86%) and Group3 (78.2%). MM2S also enables classification of MB cell lines and mouse models into their human counterparts.This package contains function for implementing the classifier onto human data and mouse data, as well as graphical rendering of the results as PCA plots and heatmaps.
Author: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Maintainer: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>
Diff between MM2S versions 1.0.0 dated 2015-06-11 and 1.0.1 dated 2015-06-17
DESCRIPTION | 10 +++---- MD5 | 18 +++++++------ NEWS |only R/MM2S.human.R | 11 ++++++++ R/MM2S.mouse.R | 12 ++++++++ R/PCARender.R | 12 ++++++++ R/PredictionsHeatmap.R | 12 ++++++++ inst |only man/MM2S.human.Rd | 2 - man/MM2S.mouse.Rd | 2 - vignettes/MM2S.Rnw | 67 ++++++++++++++++++++++++++++++++++--------------- 11 files changed, 111 insertions(+), 35 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 4.4.0 dated 2015-05-29 and 4.4.1 dated 2015-06-17
DESCRIPTION | 6 - MD5 | 30 ++++---- NEWS | 25 ++++++- R/earth.R | 20 +++-- R/earth.cv.R | 2 R/expand.arg.R | 132 +++++++++++++++++++------------------ R/lib.R | 42 ----------- R/model.matrix.earth.R | 16 ++-- R/plotd.R | 5 - inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/test.full.R | 44 ++++++++++++ inst/slowtests/test.full.Rout.save | 89 ++++++++++++++++++++++++ inst/slowtests/test.glm.R | 6 + inst/slowtests/test.glm.Rout.save | 19 ++++- man/earth.Rd | 2 16 files changed, 287 insertions(+), 151 deletions(-)
Title: Seasonal/Sequential (Instants/'Durations', Even or not) Time
Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time 'durations' are handled. Both can be regularly or unevenly spaced (overlapping 'durations' are allowed). Only 'POSIX*' format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>
Diff between timetools versions 1.6.5 dated 2014-12-08 and 1.7.0 dated 2015-06-17
DESCRIPTION | 12 +++++----- MD5 | 18 ++++++++-------- NAMESPACE | 3 ++ R/TimeInstantDataFrame.R | 40 ++++++++++++++++++++++++++++++++++-- R/TimeIntervalDataFrame.R | 41 +++++++++++++++++++++++++++++++++++-- README | 12 ++++++++++ man/TimeInstantDataFrame-class.Rd | 15 +++++++++++++ man/TimeIntervalDataFrame-class.Rd | 15 +++++++++++++ man/timetools-package.Rd | 4 +-- src/Makevars | 2 - 10 files changed, 140 insertions(+), 22 deletions(-)
Title: 3D Animated Interactive Visualizations Using SVG
Description: Creates 3D animated, interactive visualizations in Scalable Vector Graphics (SVG) format that can be viewed in a web browser.
Author: Aaron Olsen
Maintainer: Aaron Olsen <aolsen@uchicago.edu>
Diff between svgViewR versions 1.0.0 dated 2014-12-28 and 1.0.1 dated 2015-06-17
svgViewR-1.0.0/svgViewR/inst/extdata/svg_viewer_3d_n.js |only svgViewR-1.0.0/svgViewR/inst/extdata/svg_viewer_n.js |only svgViewR-1.0.1/svgViewR/DESCRIPTION | 10 svgViewR-1.0.1/svgViewR/MD5 | 32 - svgViewR-1.0.1/svgViewR/R/svgviewr.circles.R |only svgViewR-1.0.1/svgViewR/R/svgviewr.lines.R | 59 +-- svgViewR-1.0.1/svgViewR/R/svgviewr.new.R | 25 - svgViewR-1.0.1/svgViewR/R/svgviewr.paths.R |only svgViewR-1.0.1/svgViewR/R/svgviewr.pathsC.R | 2 svgViewR-1.0.1/svgViewR/R/svgviewr.points.R | 71 ++- svgViewR-1.0.1/svgViewR/R/svgviewr.pointsC.R |only svgViewR-1.0.1/svgViewR/R/svgviewr.text.R |only svgViewR-1.0.1/svgViewR/inst/extdata/control_panel.js |only svgViewR-1.0.1/svgViewR/inst/extdata/math.js |only svgViewR-1.0.1/svgViewR/inst/extdata/shape_operations.js |only svgViewR-1.0.1/svgViewR/inst/extdata/shapes.js |only svgViewR-1.0.1/svgViewR/inst/extdata/ui_functions.js | 286 +++++++++++++++ svgViewR-1.0.1/svgViewR/man/svgViewR-package.Rd | 11 svgViewR-1.0.1/svgViewR/man/svgviewr.lines.Rd | 36 - svgViewR-1.0.1/svgViewR/man/svgviewr.new.Rd | 5 svgViewR-1.0.1/svgViewR/man/svgviewr.pathsC.Rd | 2 svgViewR-1.0.1/svgViewR/man/svgviewr.points.Rd | 34 + 22 files changed, 439 insertions(+), 134 deletions(-)
Title: Facilitating Estimation of the Intraclass Correlation
Coefficient
Description: Assist in the estimation of the Intraclass Correlation Coefficient (ICC) from variance components of a one-way analysis of variance and also estimate the number of individuals or groups necessary to obtain an ICC estimate with a desired confidence interval width.
Author: Matthew Wolak [cre, aut]
Maintainer: Matthew Wolak <matthewwolak@gmail.com>
Diff between ICC versions 2.2.1 dated 2013-10-04 and 2.3.0 dated 2015-06-17
ICC-2.2.1/ICC/R/ICCbare.r |only ICC-2.2.1/ICC/R/ICCbareF.r |only ICC-2.2.1/ICC/R/ICCest.r |only ICC-2.2.1/ICC/R/Nest.r |only ICC-2.2.1/ICC/R/effort.r |only ICC-2.3.0/ICC/DESCRIPTION | 23 +++++++++++++---------- ICC-2.3.0/ICC/MD5 | 27 ++++++++++++++------------- ICC-2.3.0/ICC/NAMESPACE | 6 +++++- ICC-2.3.0/ICC/R/ICCbare.R |only ICC-2.3.0/ICC/R/ICCbareF.R |only ICC-2.3.0/ICC/R/ICCest.R |only ICC-2.3.0/ICC/R/Nest.R |only ICC-2.3.0/ICC/R/effort.R |only ICC-2.3.0/ICC/README.md |only ICC-2.3.0/ICC/man/ICC-package.Rd | 10 +++++----- ICC-2.3.0/ICC/man/ICCbare.Rd | 14 +++++++------- ICC-2.3.0/ICC/man/ICCbareF.Rd | 15 ++++++++------- ICC-2.3.0/ICC/man/ICCest.Rd | 33 ++++++++++++++++----------------- ICC-2.3.0/ICC/man/Nest.Rd | 38 +++++++++++++++++++------------------- ICC-2.3.0/ICC/man/effort.Rd | 26 ++++++++++++-------------- 20 files changed, 99 insertions(+), 93 deletions(-)
Title: An R Plug-in for the Distributed Hydrological Model GEOtop
Description: It analyzes raster maps and other information as input/output
files from the Hydrological Distributed Model GEOtop. It contains functions
and methods to import maps and other keywords from geotop.inpts file. Some
examples with simulation cases of GEOtop 2.0 are presented in the package.
Any information about the GEOtop Distributed Hydrological Model source code
is available on http://code.google.com/p/geotop/ or
https://github.com/se27xx/GEOtop. Technical details about the model are
available in Endrizzi et al, 2014
(http://www.geosci-model-dev.net/7/2831/2014/gmd-7-2831-2014.html).
Author: Emanuele Cordano, Daniele Andreis, Fabio Zottele
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>
Diff between geotopbricks versions 1.3.6 dated 2015-02-23 and 1.3.7.2 dated 2015-06-17
DESCRIPTION | 8 MD5 | 89 ++++---- NAMESPACE | 2 R/brickFromOutput3DTensor.R | 2 R/create.geotop.inpts.keywords.R | 2 R/get.keyword.value.R | 91 +++++++- R/getProjection.R | 2 R/listFromOutput3DTensor.R | 4 R/writeRasterxgeotop.R | 8 data/bondone.rda |binary inst/doc/examples/example.brickFromOutput3DTensor.R | 2 inst/doc/examples/example.geotopmeteostation.R | 2 inst/doc/examples/example.time.aggragation.R | 2 inst/png___kml.R |only man/GeotopRasterBrick-class.Rd | 28 +- man/KML-methods.Rd | 16 - man/Ops-methods.Rd | 11 - man/brick-methods.Rd | 54 +---- man/brick.decimal.formatter.Rd | 52 +---- man/brickFromOutputSoil3DTensor.Rd | 99 +++------ man/color.bar.Rd | 39 +-- man/color.bar.raster.Rd | 15 - man/create.geotop.inpts.keyword.Rd | 31 +- man/create.geotop.meteo.files.Rd | 47 +--- man/declared.geotop.inpts.keywords.Rd | 29 -- man/geotopbrick.Rd | 44 ++-- man/get.geotop.inpts.keyword.value.Rd | 208 +++++++------------- man/get.geotop.recovery.state.Rd | 25 -- man/getProjection.Rd | 14 - man/getvalues.brick.at.depth.Rd | 38 +-- man/listFromOutputSoil3DTensor.Rd | 99 ++------- man/max_value.Rd | 11 - man/min_value.Rd | 11 - man/plot-methods.Rd | 8 man/pointer.to.maps.xyz.time.Rd | 24 -- man/read.ascii.vectorized.brick.Rd | 25 -- man/read.raster.from.url.Rd | 16 - man/read.vectorized.geotop.recovery.Rd | 31 -- man/replace.keyword.Rd | 35 --- man/set.geotop.recovery.state.Rd | 12 - man/vertical.aggregate.brick.within.depth.Rd | 40 +-- man/write.ascii.vectorized.brick.Rd | 28 -- man/write.vectorized.geotop.recovery.Rd | 29 -- man/write.vectorized.variable.in.string.Rd | 21 -- man/writeRasterxGEOtop.Rd | 70 ++---- man/zoo-class.Rd | 4 46 files changed, 579 insertions(+), 849 deletions(-)