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 1.0.3 dated 2015-08-12 and 1.0.4 dated 2015-11-02
DESCRIPTION | 8 ++++---- MD5 | 28 +++++++++++++++++----------- NEWS | 5 +++++ R/PredictionsBarplot.R |only R/PredictionsDistributionBoxplot.R |only R/PredictionsDistributionPie.R |only README | 6 ++++++ inst/doc/MM2S.R | 15 +++++++++++++-- inst/doc/MM2S.Rnw | 28 ++++++++++++++++++++++++---- inst/doc/MM2S.pdf |binary inst/doc/MM2S_Vignette_FrozenCapture.pdf |binary man/MM2S.human.Rd | 4 ++-- man/MM2S.mouse.Rd | 8 ++++---- man/PCARender.Rd | 12 ++++++------ man/PredictionsBarplot.Rd |only man/PredictionsDistributionBoxplot.Rd |only man/PredictionsDistributionPie.Rd |only vignettes/MM2S.Rnw | 28 ++++++++++++++++++++++++---- 18 files changed, 105 insertions(+), 37 deletions(-)
Title: Data-Limited Methods Toolkit
Description: Simulation testing and implementation of data-limited fishery stock assessment methods.
Author: Tom Carruthers
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 2.1 dated 2015-11-01 and 2.1.1 dated 2015-11-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/MSE_source.R | 2 +- inst/doc/DLMtool.Rnw | 9 +++++++-- inst/doc/DLMtool.pdf |binary man/DLMtool-package.Rd | 4 ++-- vignettes/DLMtool.Rnw | 9 +++++++-- 7 files changed, 27 insertions(+), 17 deletions(-)
Title: Epidemiological Data Display Package
Description: Package for data exploration and result presentation.
Full 'epicalc' package with data management functions is available
at the author's repository.
Author: Virasakdi Chongsuvivatwong <cvirasak@medicine.psu.ac.th>
Maintainer: Virasakdi Chongsuvivatwong <cvirasak@medicine.psu.ac.th>
Diff between epiDisplay versions 3.2.0.6 dated 2015-07-01 and 3.2.2.0 dated 2015-11-02
DESCRIPTION | 8 - MD5 | 13 +- NAMESPACE | 37 +++--- R/epiDisplay.R | 260 +++++++++++++++++++++++++++++++++---------------- man/matchTab.rd | 4 man/print.matchTab.rd |only man/print.statStack.rd |only man/statStack.rd |only man/tableStack.rd | 22 +++- 9 files changed, 228 insertions(+), 116 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.0-7 dated 2015-09-06 and 1.1-1 dated 2015-11-02
ChangeLog | 1370 ------------------------------------ DESCRIPTION | 8 MD5 | 31 R/make_EPSG.R | 9 configure | 18 inst/ChangeLog | 1370 ------------------------------------ inst/SVN_VERSION | 2 inst/doc/OGR_shape_encoding.pdf |binary inst/etc/obj_with_comments.RData |only inst/etc/obj_without_comments.RData |only inst/etc/test_dfs.RData |only man/readOGR.Rd | 2 man/showWKT.Rd | 2 man/writeOGR.Rd | 21 src/OGR_write.cpp | 226 ++++- src/ogrdrivers.cpp | 10 src/ogrsource.cpp | 2 tests/tripup.R |only tests/tripup.Rout.save |only 19 files changed, 242 insertions(+), 2829 deletions(-)
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees.
This package includes a shiny interface which can be started from R using
'treescapeServer()'.
Author: Thibaut Jombart [aut],
Michelle Kendall [aut, cre],
Jacob Almagro-Garcia [aut],
Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>
Diff between treescape versions 1.8.14 dated 2015-10-30 and 1.8.15 dated 2015-11-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 ++ R/servers.R | 2 ++ inst/shiny/server.R | 5 ----- inst/shiny/ui.R | 2 ++ 6 files changed, 15 insertions(+), 14 deletions(-)
Title: Implementation of Unobserved Components Model (UCM)
Description: Unobserved Components Models (introduced in Harvey, A. (1989),
Forecasting, structural time series models and the Kalman filter, Cambridge
New York: Cambridge University Press) decomposes a time series into
components such as trend, seasonal, cycle, and the regression effects due
to predictor series which captures the salient features of the series to
predict its behavior.
Author: Kaushik Roy Chowdhury
Maintainer: Kaushik Roy Chowdhury <kaushikrch@gmail.com>
Diff between rucm versions 0.4 dated 2014-09-07 and 0.5 dated 2015-11-02
rucm-0.4/rucm/vignettes/figure |only rucm-0.5/rucm/DESCRIPTION | 12 - rucm-0.5/rucm/MD5 | 32 +-- rucm-0.5/rucm/NAMESPACE | 9 - rucm-0.5/rucm/NEWS | 6 rucm-0.5/rucm/R/predict.ucm.R | 5 rucm-0.5/rucm/R/print.ucm.R | 1 rucm-0.5/rucm/R/ucm.R | 256 ++++++++++++++++------------- rucm-0.5/rucm/README.md |only rucm-0.5/rucm/build/vignette.rds |binary rucm-0.5/rucm/inst/doc/rucm_vignettes.R | 1 rucm-0.5/rucm/inst/doc/rucm_vignettes.Rmd | 7 rucm-0.5/rucm/inst/doc/rucm_vignettes.html | 21 -- rucm-0.5/rucm/man/predict.ucm.Rd | 8 rucm-0.5/rucm/man/print.ucm.Rd | 3 rucm-0.5/rucm/man/rucm-package.Rd | 17 + rucm-0.5/rucm/man/ucm.Rd | 3 rucm-0.5/rucm/vignettes/rucm_vignettes.Rmd | 7 18 files changed, 218 insertions(+), 170 deletions(-)
Title: Multivariate Probit Models
Description: Tools for estimating multivariate probit models,
calculating conditional and unconditional expectations,
and calculating marginal effects on conditional and unconditional
expectations.
Author: Arne Henningsen <arne.henningsen@gmail.com>
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between mvProbit versions 0.1-4 dated 2015-09-03 and 0.1-8 dated 2015-11-02
DESCRIPTION | 8 +-- MD5 | 12 ++--- R/logLik.mvProbit.R | 2 R/summary.mvProbit.R | 2 man/mvProbit.Rd | 4 - tests/mvProbitEst.R | 34 +++++++------- tests/mvProbitEst.Rout.save | 104 ++++++++++++++++++++++---------------------- 7 files changed, 83 insertions(+), 83 deletions(-)
Title: Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair with Lapack
Description: Functions to compute generalized eigenvalues and eigenvectors,
the generalized Schur decomposition and
the generalized Singular Value Decomposition of a matrix pair,
using Lapack routines.
Author: Berend Hasselman [cre, aut],
Lapack authors [aut, cph]
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between geigen versions 1.7 dated 2015-10-15 and 1.8 dated 2015-11-02
geigen-1.7/geigen/tests/tgeigen1.Rout |only geigen-1.7/geigen/tests/tgeigen2.Rout |only geigen-1.7/geigen/tests/tgqz1.Rout |only geigen-1.7/geigen/tests/tgqz2.Rout |only geigen-1.7/geigen/tests/tgqz3.Rout |only geigen-1.7/geigen/tests/tgqz4.Rout |only geigen-1.7/geigen/tests/tgqz5.Rout |only geigen-1.7/geigen/tests/tgqz6.Rout |only geigen-1.7/geigen/tests/tgsvd5.R |only geigen-1.7/geigen/tests/tgsvd5.Rout.save |only geigen-1.7/geigen/tests/tgsvd6.R |only geigen-1.7/geigen/tests/tgsvd6.Rout.save |only geigen-1.7/geigen/tests/tgsvd7.R |only geigen-1.7/geigen/tests/tgsvd7.Rout.save |only geigen-1.7/geigen/tests/tgsvd8.R |only geigen-1.7/geigen/tests/tgsvd8.Rout.save |only geigen-1.8/geigen/DESCRIPTION | 8 +- geigen-1.8/geigen/MD5 | 52 +++++++------------ geigen-1.8/geigen/NAMESPACE | 4 - geigen-1.8/geigen/NEWS | 4 + geigen-1.8/geigen/R/gsvd.R | 67 +++++++++++++++++-------- geigen-1.8/geigen/inst/COPYRIGHTS | 1 geigen-1.8/geigen/man/geigen-package.Rd | 4 - geigen-1.8/geigen/man/geigen.Rd | 2 geigen-1.8/geigen/man/gqz.Rd | 2 geigen-1.8/geigen/man/gsvd.Rd | 41 +++++++++++---- geigen-1.8/geigen/src/xzggsvd.f |only geigen-1.8/geigen/src/zggsvdall.f |only geigen-1.8/geigen/tests/testgsvd.R | 11 +++- geigen-1.8/geigen/tests/tgqz2.Rout.save | 8 +- geigen-1.8/geigen/tests/tgsvd2.R | 12 +++- geigen-1.8/geigen/tests/tgsvd2.Rout.save | 40 ++++++++++---- geigen-1.8/geigen/tests/tgsvd3.R | 29 ++++++++-- geigen-1.8/geigen/tests/tgsvd3.Rout.save | 60 ++++++++++++++-------- geigen-1.8/geigen/tests/tgsvd4.R | 54 ++++++++++++++++++-- geigen-1.8/geigen/tests/tgsvd4.Rout.save | 83 +++++++++++++++++++++++-------- 36 files changed, 332 insertions(+), 150 deletions(-)
Title: Export Tables to LaTeX or HTML
Description: Coerce data to LaTeX and HTML tables.
Author: David B. Dahl <dahl@stat.byu.edu>
Maintainer: David Scott <d.scott@auckland.ac.nz>
Diff between xtable versions 1.7-4 dated 2014-09-12 and 1.8-0 dated 2015-11-02
xtable-1.7-4/xtable/inst/doc/xtableGallery.snw |only xtable-1.7-4/xtable/vignettes/xtableGallery.snw |only xtable-1.8-0/xtable/DESCRIPTION | 15 xtable-1.8-0/xtable/MD5 | 41 xtable-1.8-0/xtable/NAMESPACE | 14 xtable-1.8-0/xtable/NEWS | 35 xtable-1.8-0/xtable/R/autoformat.R |only xtable-1.8-0/xtable/R/toLatex.R | 2 xtable-1.8-0/xtable/R/xtable.R | 93 + xtable-1.8-0/xtable/build/vignette.rds |binary xtable-1.8-0/xtable/data/tli.txt.gz |binary xtable-1.8-0/xtable/inst/doc/margintable.R | 13 xtable-1.8-0/xtable/inst/doc/margintable.Rnw | 13 xtable-1.8-0/xtable/inst/doc/margintable.pdf |binary xtable-1.8-0/xtable/inst/doc/xtableGallery.R | 744 ++++----------- xtable-1.8-0/xtable/inst/doc/xtableGallery.Rnw |only xtable-1.8-0/xtable/inst/doc/xtableGallery.pdf |binary xtable-1.8-0/xtable/man/autoformat.Rd |only xtable-1.8-0/xtable/man/print.xtable.Rd | 89 - xtable-1.8-0/xtable/man/table.attributes.Rd | 7 xtable-1.8-0/xtable/man/tli.Rd | 3 xtable-1.8-0/xtable/man/xtable.Rd | 56 - xtable-1.8-0/xtable/tests/test.xalign.xdigits.xdisplay.R |only xtable-1.8-0/xtable/vignettes/margintable.Rnw | 13 xtable-1.8-0/xtable/vignettes/xtableGallery.Rnw |only 25 files changed, 432 insertions(+), 706 deletions(-)
Title: Interface to Colombos Compendia using the Exposed REST API
Description: Provides programmatic access to Colombos, a web based
interface for exploring and analyzing comprehensive organism-specific
cross-platform expression compendia of bacterial organisms.
Author: Paolo Sonego <paolo.sonego@fmach.it>
Maintainer: Paolo Sonego <paolo.sonego@fmach.it>
Diff between Rcolombos versions 1.5.3 dated 2015-09-07 and 2.0.2 dated 2015-11-02
DESCRIPTION | 8 +- MD5 | 38 ++++++------ NAMESPACE | 2 R/Rcolombos.R | 34 ++++++----- R/utilities.R | 111 ++++++++++++++++++++++++++++-------- R/zzz.R | 6 - README.md |only man/Rcolombos.Rd |only man/advanced_search.Rd | 2 man/advanced_search_by_both.Rd | 2 man/advanced_search_by_contrasts.Rd | 2 man/advanced_search_by_genes.Rd | 2 man/getCompendium.Rd | 12 ++- man/get_contrast_annotations.Rd |only man/listAnnotationTypes.Rd | 2 man/listContrasts.Rd | 2 man/listEntities.Rd | 2 man/listGenes.Rd | 2 man/listOrganisms.Rd | 4 - man/parseCompendium.Rd | 12 ++- man/quick_search.Rd | 2 man/switchVersion.Rd |only 22 files changed, 165 insertions(+), 80 deletions(-)
Title: Unsampled Data in R for Google Analytics Premium Accounts
Description: It fires a query to the API to get the unsampled data in R for Google Analytics Premium Accounts. It retrieves data from the Google drive document and stores it into the local drive. The path to the excel file is returned by this package. The user can read data from the excel file into R using read.csv() function.
Author: Jalpa Joshi Dave
Maintainer: Jalpa Joshi Dave <jalpa@tatvic.com>
Diff between RGoogleAnalyticsPremium versions 0.1 dated 2015-10-29 and 0.1.1 dated 2015-11-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- demo/data_extraction_final.R | 8 +++----- 3 files changed, 8 insertions(+), 10 deletions(-)
More information about RGoogleAnalyticsPremium at CRAN
Permanent link
Title: Management, Display, and Processing of Medical Imaging Data
Description: Provide a compact storage for medical imaging data with access and display possibilities. Basic tools for processing brain imaging data are proposed like extraction of brain voxels, morphological image segmentation, and filtering / normalization of contrast parameters. Specific tools are also provided for blood perfusion imaging to calculate hypoperfusion and reperfusion volumes.
Author: Brice Ozenne
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>
Diff between MRIaggr versions 1.1.2 dated 2015-05-12 and 1.1.3 dated 2015-11-02
MRIaggr-1.1.2/MRIaggr/R/Associated_functions.R |only MRIaggr-1.1.2/MRIaggr/R/GR_functions.R |only MRIaggr-1.1.2/MRIaggr/R/Generic_functions.R |only MRIaggr-1.1.2/MRIaggr/inst/calcCriteriaGR.Rd |only MRIaggr-1.1.2/MRIaggr/inst/calcSigmaGR.Rd |only MRIaggr-1.1.2/MRIaggr/man/Carto3D2MRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/EDK.Rd |only MRIaggr-1.1.2/MRIaggr/man/GRalgo.Rd |only MRIaggr-1.1.2/MRIaggr/man/MRIaggr-package.Rd |only MRIaggr-1.1.2/MRIaggr/man/MRIaggr.Pat1_red.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocClinic.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocContrast.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocDescStats.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocHemisphere.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocNormalization.Rd |only MRIaggr-1.1.2/MRIaggr/man/allocTable.Rd |only MRIaggr-1.1.2/MRIaggr/man/array2df.Rd |only MRIaggr-1.1.2/MRIaggr/man/boxplotMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcAUPRC.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcBrainMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcContro_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcControlateral.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcDistMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcDistTissues.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcFilter.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGR.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGroupsCoords.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGroupsCoords_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGroupsMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGroupsW.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcGroupsW_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcHemi_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcHemisphere.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcNormalization.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcROCthreshold.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcRadius_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcRegionaContrast.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcSmoothMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcTableHypoReperf.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcTableLesion.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcThresholdMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcTissueType.Rd |only MRIaggr-1.1.2/MRIaggr/man/calcW.Rd |only MRIaggr-1.1.2/MRIaggr/man/constCarto3D.Rd |only MRIaggr-1.1.2/MRIaggr/man/constCompressMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/constLatex.Rd |only MRIaggr-1.1.2/MRIaggr/man/constMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/constReduceMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/df2array.Rd |only MRIaggr-1.1.2/MRIaggr/man/filtrage2D_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/filtrage2Dmed_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/filtrage3D_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/filtrage3Dmed_cpp.Rd |only MRIaggr-1.1.2/MRIaggr/man/heatmapMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/initCol.Rd |only MRIaggr-1.1.2/MRIaggr/man/initConstLatex.Rd |only MRIaggr-1.1.2/MRIaggr/man/initDisplayWindow.Rd |only MRIaggr-1.1.2/MRIaggr/man/initFilter.Rd |only MRIaggr-1.1.2/MRIaggr/man/initGR.Rd |only MRIaggr-1.1.2/MRIaggr/man/initIndex.Rd |only MRIaggr-1.1.2/MRIaggr/man/initMask.Rd |only MRIaggr-1.1.2/MRIaggr/man/initNeighborhood.Rd |only MRIaggr-1.1.2/MRIaggr/man/initNum.Rd |only MRIaggr-1.1.2/MRIaggr/man/initParameter.Rd |only MRIaggr-1.1.2/MRIaggr/man/initWindow.Rd |only MRIaggr-1.1.2/MRIaggr/man/legendMRI.Rd |only MRIaggr-1.1.2/MRIaggr/man/multiplot.Rd |only MRIaggr-1.1.2/MRIaggr/man/outline.Rd |only MRIaggr-1.1.2/MRIaggr/man/outlineMRIaggr.Rd |only MRIaggr-1.1.2/MRIaggr/man/plotDistClass.Rd |only MRIaggr-1.1.2/MRIaggr/man/plotLesion3D.Rd |only MRIaggr-1.1.2/MRIaggr/man/plotMRI.Rd |only MRIaggr-1.1.2/MRIaggr/man/plotOutline.Rd |only MRIaggr-1.1.2/MRIaggr/man/plotTableLesion.Rd |only MRIaggr-1.1.2/MRIaggr/man/pointsHemisphere.Rd |only MRIaggr-1.1.2/MRIaggr/man/readMRI.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectClinic.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectContrast.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectCoords.Rd |only MRIaggr-1.1.2/MRIaggr/man/selectDefault_value.Rd |only 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477 MRIaggr-1.1.3/MRIaggr/R/Class_MRIaggr.R | 9119 +++++----- MRIaggr-1.1.3/MRIaggr/R/Functions_AssociatedClass.R |only MRIaggr-1.1.3/MRIaggr/R/Functions_GR.R |only MRIaggr-1.1.3/MRIaggr/R/Functions_Miscellaneous.R |only MRIaggr-1.1.3/MRIaggr/R/Functions_Options.R |only MRIaggr-1.1.3/MRIaggr/R/Functions_Potts.R |only MRIaggr-1.1.3/MRIaggr/R/Functions_Valid.R |only MRIaggr-1.1.3/MRIaggr/R/Generic_Functions.R |only MRIaggr-1.1.3/MRIaggr/R/RcppExports.R | 48 MRIaggr-1.1.3/MRIaggr/data/MRIaggr.Pat1_red.RData |binary MRIaggr-1.1.3/MRIaggr/demo/Analysis.R | 108 MRIaggr-1.1.3/MRIaggr/demo/ExtractNifti.R | 95 MRIaggr-1.1.3/MRIaggr/demo/preProcessing.R | 282 MRIaggr-1.1.3/MRIaggr/inst/Data_Tests |only MRIaggr-1.1.3/MRIaggr/inst/Functions_Segmentation.R |only MRIaggr-1.1.3/MRIaggr/inst/Functions_UserSegmentation.R |only MRIaggr-1.1.3/MRIaggr/inst/List_of_arguments.R | 3049 +-- MRIaggr-1.1.3/MRIaggr/inst/NEWS | 28 MRIaggr-1.1.3/MRIaggr/inst/TODO | 9 MRIaggr-1.1.3/MRIaggr/inst/hist |only 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insertions(+), 6664 deletions(-)
Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals based on the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 doi:10.1002/sim.2897 or Baker and Jackson, 2008 doi:10.1007/s10729-007-9041-8) or mixtures of normals (Beath, 2014 doi:10.1002/jrsm.1114).
Author: Ken Beath [aut, cre], Ben Bolker [aut], R Development Core Team [aut]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between metaplus versions 0.7-4 dated 2015-07-03 and 0.7-5 dated 2015-11-02
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Title: Visualizes Random Forests with Feature Contributions
Description: Enables users to form appropriate visualizations of high dimensional mapping curvatures of random forests.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.8.6 dated 2015-09-13 and 1.8.8 dated 2015-11-02
forestFloor-1.8.6/forestFloor/R/forestFloor_multiClass.R |only forestFloor-1.8.8/forestFloor/DESCRIPTION | 10 forestFloor-1.8.8/forestFloor/MD5 | 80 - forestFloor-1.8.8/forestFloor/NAMESPACE | 130 +- forestFloor-1.8.8/forestFloor/R/RcppExports.R | 22 forestFloor-1.8.8/forestFloor/R/append.overwrite.alists.R | 18 forestFloor-1.8.8/forestFloor/R/as.numeric.factor.R | 12 forestFloor-1.8.8/forestFloor/R/box.outliers.R | 58 - forestFloor-1.8.8/forestFloor/R/convolute_ff.R | 72 - forestFloor-1.8.8/forestFloor/R/convolute_ff2.R | 198 +-- forestFloor-1.8.8/forestFloor/R/fcol.R | 466 ++++---- forestFloor-1.8.8/forestFloor/R/forestFloor_randomForest_multiClass.R |only forestFloor-1.8.8/forestFloor/R/forestFloor_randomForest_regression.R |only forestFloor-1.8.8/forestFloor/R/forestFloor_source.R | 224 ---- forestFloor-1.8.8/forestFloor/R/ggPlotForestFloor.R | 98 - forestFloor-1.8.8/forestFloor/R/plot.forestFloor_multiClass.R | 184 +-- forestFloor-1.8.8/forestFloor/R/plot.forestFloor_regression.R | 244 ++-- forestFloor-1.8.8/forestFloor/R/plot_simplex3.R | 260 ++-- forestFloor-1.8.8/forestFloor/R/print.forestFloor_regression.R | 14 forestFloor-1.8.8/forestFloor/R/show3d.R | 342 +++--- forestFloor-1.8.8/forestFloor/R/vec.plot.R | 76 - forestFloor-1.8.8/forestFloor/man/append.overwrite.alists.Rd | 90 - forestFloor-1.8.8/forestFloor/man/as.numeric.factor.Rd | 84 - forestFloor-1.8.8/forestFloor/man/box.outliers.Rd | 120 +- forestFloor-1.8.8/forestFloor/man/convolute_ff.Rd | 160 +-- forestFloor-1.8.8/forestFloor/man/convolute_ff2.Rd | 180 +-- forestFloor-1.8.8/forestFloor/man/convolute_grid.Rd | 352 +++--- forestFloor-1.8.8/forestFloor/man/fcol.Rd | 266 ++--- forestFloor-1.8.8/forestFloor/man/forestFloor-package.Rd | 74 - forestFloor-1.8.8/forestFloor/man/forestFloor.Rd | 509 ++++----- forestFloor-1.8.8/forestFloor/man/ggPlotForestFloor.Rd | 136 +- forestFloor-1.8.8/forestFloor/man/ggplotGrob.Rd | 30 forestFloor-1.8.8/forestFloor/man/plot.forestFloor.Rd | 524 +++++----- forestFloor-1.8.8/forestFloor/man/plot_simplex3.Rd | 270 ++--- forestFloor-1.8.8/forestFloor/man/print.forestFloor.Rd | 112 +- forestFloor-1.8.8/forestFloor/man/recTree.Rd | 250 ++-- forestFloor-1.8.8/forestFloor/man/show3d.Rd | 412 +++---- forestFloor-1.8.8/forestFloor/man/vec.plot.Rd | 192 +-- forestFloor-1.8.8/forestFloor/tests/ggplotUsage.R | 38 forestFloor-1.8.8/forestFloor/tests/rfPermute_supported.R |only forestFloor-1.8.8/forestFloor/tests/stdUsage.R | 106 +- forestFloor-1.8.8/forestFloor/tests/testBinaryClass.R | 102 - forestFloor-1.8.8/forestFloor/tests/testMultiClass.cpp.R | 172 +-- 43 files changed, 3296 insertions(+), 3391 deletions(-)
Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Description: ExPANdS characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in EXPANDS version 1.6 include: (1) So far mutations had been assigned to maximal one subpopulation. However mutations may not be exclusive to the assigned subpopulation but may also be present in smaller, descending subpopulations. This version of expands decides whether or not this is the case leveraging the predicted phylogenetic structure of the subpopulation composition. (2) Included homozygous deletion as potential scenario when modeling (SNV,CNV) pairs with overlapping genomic location, that are propagated during distinct clonal expansions. (3) Optimized solution to improve sensitivity at cell-frequency distribution margins. Need for improvement was because subpopulation detection sensitivity correlates to centrality of subpopulation size during clustering. Tolerance of copy number and allele frequency measurement errors must be higher for marginal cell-frequencies than for central cell-frequencies, in order to counteract the reduced cluster detection sensitivity at the cell-frequency distribution margins. This is only relevant during subpopulation detection (SNV clustering), cell-frequency independent error tolerance still applies during SNV assignment. (4) Fixed a bug where incorrect data matrix conversion could occur when handing non-numerical matrix as parameter to function runExPANdS. Further documentation and FAQ around ExPANdS is available at http://dna-discovery.stanford.edu/software/expands.
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>
Diff between expands versions 1.5 dated 2014-09-28 and 1.6 dated 2015-11-02
expands-1.5/expands/java/ExPANdS.java |only expands-1.6/expands/DESCRIPTION | 16 expands-1.6/expands/MD5 | 56 - expands-1.6/expands/NAMESPACE | 5 expands-1.6/expands/R/assignMutations.R | 255 ++++- expands-1.6/expands/R/assignQuantityToSP.R | 66 - expands-1.6/expands/R/buildMultiSamplePhylo.R | 64 + expands-1.6/expands/R/buildPhylo.R | 224 +++-- expands-1.6/expands/R/cellfrequency_pdf.R | 59 - expands-1.6/expands/R/clusterCellFrequencies.R | 474 +++++------ expands-1.6/expands/R/computeCellFrequencyDistributions.R | 96 +- expands-1.6/expands/R/plotSPs.R | 125 +- expands-1.6/expands/R/runExPANdS.R | 421 +++++---- expands-1.6/expands/inst/doc/expands.R | 43 expands-1.6/expands/inst/doc/expands.Rnw | 50 - expands-1.6/expands/inst/doc/expands.pdf |binary expands-1.6/expands/inst/java/expands.jar |binary expands-1.6/expands/java/expands.jar |only expands-1.6/expands/man/assignMutations.Rd | 33 expands-1.6/expands/man/assignQuantityToSP.Rd | 30 expands-1.6/expands/man/buildMultiSamplePhylo.Rd | 26 expands-1.6/expands/man/buildPhylo.Rd | 22 expands-1.6/expands/man/cellfrequency_pdf.Rd | 48 - expands-1.6/expands/man/clusterCellFrequencies.Rd | 8 expands-1.6/expands/man/computeCellFrequencyDistributions.Rd | 9 expands-1.6/expands/man/plotSPs.Rd | 9 expands-1.6/expands/man/roi.Rd | 2 expands-1.6/expands/man/runExPANdS.Rd | 42 expands-1.6/expands/man/snv.Rd | 4 expands-1.6/expands/vignettes/expands.Rnw | 48 - 30 files changed, 1288 insertions(+), 947 deletions(-)
Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data analysis
by a unified model specification, along with some data manipulation functions.
This package covers fitting of variety models including Cox regression models,
linear regression models, Poisson regression models, logistic models and
others whose likelihood is expressed in negative binomial, gamma and Weibull
distributions.
Author: Kazutaka Doi [aut,cre],
Kei Sakabe [ctb],
Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>
Diff between epifit versions 0.0.3 dated 2015-10-01 and 0.0.4 dated 2015-11-02
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++++++++--------------- NAMESPACE | 7 +++++++ NEWS | 10 ++++++++++ R/AIC.epifit.R | 6 +++--- R/calcAge.R |only R/convertNA.R |only R/countNA.R |only R/epifit-package.R | 10 ++++++++-- R/epifit.R | 4 ++++ R/extractVariable.R |only R/modules.R | 8 ++++---- R/print.epifit.R | 4 ++-- R/pullOneValue.R |only R/pytable.R | 7 +++---- R/removeVariable.R |only man/AIC.epifit.Rd | 10 +++++----- man/calcAge.Rd |only man/convertNA.Rd |only man/countNA.Rd |only man/epifit-package.Rd | 10 ++++++++-- man/epifit.Rd | 4 ++++ man/extractVariable.Rd |only man/print.epifit.Rd | 2 +- man/pullOneValue.Rd |only man/pytable.Rd | 9 +++------ man/removeVariable.Rd |only src/select.h | 4 +--- 28 files changed, 94 insertions(+), 51 deletions(-)