Title: Multiple Sclerosis Lesion Segmentation using Magnetic Resonance
Imaging (MRI)
Description: Trains and makes predictions from the OASIS method, described in
detail in the paper "OASIS is Automated Statistical Inference for Segmentation,
with applications to multiple sclerosis lesion segmentation in MRI"
<doi:10.1016/j.nicl.2013.03.002>.
OASIS is a method for multiple sclerosis (MS)
lesion segmentation on structural magnetic resonance image (MRI) studies. OASIS
creates probability maps of lesion presence using the FLAIR, T2, T1, and PD
structural MRI volumes. This packages allows for training of the OASIS model
and prediction of OASIS probability maps from a trained model with user supplied
studies that have a gold standard lesion segmentation masks. The package will
also create OASIS probability maps for MRI studies using the OASIS model from
the OASIS paper if no gold standard lesion segmentation masks are available.
Author: Elizabeth M. Sweeney [aut, cre],
John Muschelli [aut],
R. Taki Shinohara [aut]
Maintainer: Elizabeth M. Sweeney <emsweene@jhsph.edu>
Diff between oasis versions 0.99.5 dated 2015-12-26 and 2.1 dated 2016-09-29
DESCRIPTION | 34 ++-- MD5 | 30 ++- NAMESPACE | 26 ++- R/correct_image_dim.R | 18 +- R/oasis_erode.R |only R/oasis_predict.R | 251 +++++++++++-------------------- R/oasis_preproc.R | 86 ++++++---- R/oasis_train_dataframe.R | 342 ++++++++++++++++++++++++++++--------------- R/oasis_training.R | 54 +++--- R/voxel_selection.R | 49 +++--- man/correct_image_dim.Rd | 10 - man/oasis_erode.Rd |only man/oasis_predict.Rd | 54 ++---- man/oasis_preproc.Rd | 25 +-- man/oasis_train_dataframe.Rd | 51 +++--- man/oasis_training.Rd | 21 +- man/voxel_selection.Rd | 23 +- 17 files changed, 579 insertions(+), 495 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 1.9.17 dated 2016-06-13 and 1.10.17 dated 2016-09-29
DESCRIPTION | 16 MD5 | 103 NAMESPACE | 7 R/RcppExports.R | 2 R/metrics.R | 3 R/plotTreeDiff.R | 49 R/servers.R | 1 R/transmissionTrees.R |only R/treescape.R | 6 README.md | 55 build/vignette.rds |binary inst/doc/DengueVignette.R | 2 inst/doc/DengueVignette.Rmd | 2 inst/doc/DengueVignette.html | 146 inst/doc/TransmissionTreesVignette.R |only inst/doc/TransmissionTreesVignette.Rmd |only inst/doc/TransmissionTreesVignette.html |only inst/doc/treescape.R | 5 inst/doc/treescape.Rmd | 28 inst/doc/treescape.html | 3013 ++++++++++++++++++- inst/shiny/server.R | 12 inst/shiny/ui.R | 30 man/findMRCIs.Rd |only man/plotTreeDiff.Rd | 15 man/treescape.Rd | 1 man/wiwMedTree.Rd |only man/wiwTreeDist.Rd |only src/RcppExports.cpp | 4 vignettes/DengueVignette.Rmd | 2 vignettes/TransmissionTreesVignette.Rmd |only vignettes/figs/BEASTtree_diffs-2.png |binary vignettes/figs/compare_BEAST_to_other_trees-1.png |binary vignettes/figs/compare_BEAST_to_other_trees-2.png |binary vignettes/figs/compare_BEAST_to_other_trees-3.png |binary vignettes/figs/compare_trees_NJ_v_ML-1.png |binary vignettes/figs/construction.png |only vignettes/figs/distances_readme-1.png |binary vignettes/figs/distances_readme-2.png |binary vignettes/figs/findgroves-with-emphasis_readme-1.png |binary vignettes/figs/igraph_options-1.png |only vignettes/figs/igraph_tree1-1.png |only vignettes/figs/plotgroves2_readme-1.png |binary vignettes/figs/plotgroves2_readme-2.png |binary vignettes/figs/plotgroves2_readme-3.png |binary vignettes/figs/plotgroves_readme-1.png |binary vignettes/figs/trees2_and_3-1.png |only vignettes/figs/trees2_and_3-2.png |only vignettes/figs/wiwMedTreePlot-1.png |only vignettes/figs/wiw_MDS1000-1.png |only vignettes/figs/woodmice-tip-emphasis_readme-1.png |binary vignettes/figs/woodmiceCluster1_readme-1.png |binary vignettes/figs/woodmiceMedian_readme-1.png |binary vignettes/figs/woodmicePlots_readme-1.png |binary vignettes/figs/woodmicePlots_readme-2.png |binary vignettes/figs/woodmicePlots_readme-3.png |binary vignettes/figs/woodmice_plotTreeDiff-1.png |binary vignettes/figs/woodmice_plotTreeDiff-2.png |binary vignettes/figs/woodmice_plotTreeDiff_readme-1.png |binary vignettes/figs/woodmice_plotTreeDiff_readme-2.png |binary vignettes/treescape.Rmd | 28 60 files changed, 3317 insertions(+), 213 deletions(-)
Title: Geometric Morphometric Tools for Paleobiology
Description: Fill missing symmetrical data with mirroring, calculate Procrustes alignments with or without scaling, and compute standard or vector correlation and covariance matrices (congruence coefficients) of 3D landmarks. Tolerates missing data for all analyses.
Author: Tim Lucas, Anjali Goswami
Maintainer: Tim Lucas <timcdlucas@gmail.com>
Diff between paleomorph versions 0.1.2 dated 2016-08-08 and 0.1.3 dated 2016-09-29
DESCRIPTION | 9 +++++---- MD5 | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-)
Title: Functions for Calibrating Control Charts
Description: Calibration of thresholds of control charts such as
CUSUM charts based on past data, taking estimation error into account.
Author: Axel Gandy <a.gandy@imperial.ac.uk> and Jan Terje Kvaloy
<jan.t.kvaloy@uis.no>.
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>
Diff between spcadjust versions 1.0 dated 2015-11-21 and 1.1 dated 2016-09-29
DESCRIPTION | 8 +-- MD5 | 57 ++++++++++++------------ R/data.R |only R/main.R | 2 R/shewhart.R | 2 data |only inst/NEWS.Rd | 6 ++ inst/doc/CUSUM_LinearRegression.Rmd | 28 ++++++----- inst/doc/CUSUM_LinearRegression.html | 27 +++++------ inst/doc/CUSUM_LogisticRegression.Rmd | 34 +++++++------- inst/doc/CUSUM_LogisticRegression.html | 34 +++++++------- inst/doc/CUSUM_NormalNormal.R | 4 - inst/doc/CUSUM_NormalNormal.Rmd | 37 ++++++++------- inst/doc/CUSUM_NormalNormal.html | 41 +++++++++-------- inst/doc/EWMA_NormalNormal.R | 8 --- inst/doc/EWMA_NormalNormal.Rmd | 35 +++++++++----- inst/doc/EWMA_NormalNormal.html | 37 +++++++++++---- inst/doc/Extensions.R | 7 +- inst/doc/Extensions.Rmd | 57 +++++++++++++++++++----- inst/doc/Extensions.html | 78 ++++++++++++++++++++++++--------- inst/doc/Shewhart_NormalNormal.R | 6 +- inst/doc/Shewhart_NormalNormal.Rmd | 31 +++++++------ inst/doc/Shewhart_NormalNormal.html | 39 ++++++++-------- man/SPCproperty.Rd | 2 man/cardiacsurgery.Rd |only vignettes/CUSUM_LinearRegression.Rmd | 28 ++++++----- vignettes/CUSUM_LogisticRegression.Rmd | 34 +++++++------- vignettes/CUSUM_NormalNormal.Rmd | 37 ++++++++------- vignettes/EWMA_NormalNormal.Rmd | 35 +++++++++----- vignettes/Extensions.Rmd | 57 +++++++++++++++++++----- vignettes/Shewhart_NormalNormal.Rmd | 31 +++++++------ 31 files changed, 492 insertions(+), 310 deletions(-)
More information about scanstatistics at CRAN
Permanent link
Title: Nonparametric Spatial Statistics
Description: Multidimensional nonparametric spatio-temporal (geo)statistics.
S3 classes and methods for multidimensional: linear binning,
local polynomial kernel regression, density and variogram estimation.
Nonparametric methods for trend and variogram inference.
Author: Ruben Fernandez-Casal
Maintainer: Ruben Fernandez-Casal <rubenfcasal@gmail.com>
Diff between npsp versions 0.3-6 dated 2014-10-20 and 0.5-3 dated 2016-09-29
npsp-0.3-6/npsp/R/h.cv.r |only npsp-0.3-6/npsp/inst/CHANGES |only npsp-0.5-3/npsp/ChangeLog |only npsp-0.5-3/npsp/DESCRIPTION | 23 npsp-0.5-3/npsp/MD5 | 141 ++- npsp-0.5-3/npsp/NAMESPACE | 235 +++--- npsp-0.5-3/npsp/R/bin.data.R | 53 + npsp-0.5-3/npsp/R/coords.R | 40 - npsp-0.5-3/npsp/R/cov.R | 7 npsp-0.5-3/npsp/R/cpu.time.R | 9 npsp-0.5-3/npsp/R/grid.par.R | 5 npsp-0.5-3/npsp/R/h.cv.R |only npsp-0.5-3/npsp/R/interp.R | 24 npsp-0.5-3/npsp/R/locpol.bin.R | 794 ++++++++++----------- npsp-0.5-3/npsp/R/mask.R |only npsp-0.5-3/npsp/R/np.den.R | 54 + npsp-0.5-3/npsp/R/np.svar.R | 19 npsp-0.5-3/npsp/R/npsp-geoR.R | 18 npsp-0.5-3/npsp/R/npsp-gstat.R | 5 npsp-0.5-3/npsp/R/npsp-package.R | 6 npsp-0.5-3/npsp/R/npsp-plot.R | 3 npsp-0.5-3/npsp/R/npsp-rules.R |only npsp-0.5-3/npsp/R/rgraphics.R | 9 npsp-0.5-3/npsp/R/simage.R | 427 +++++------ npsp-0.5-3/npsp/R/spersp.R | 9 npsp-0.5-3/npsp/R/splot.R | 4 npsp-0.5-3/npsp/R/spoints.R | 300 ++++---- npsp-0.5-3/npsp/R/svar.bin.R | 22 npsp-0.5-3/npsp/R/svarmod.R | 10 npsp-0.5-3/npsp/R/svarmod.sb.R | 257 ++++-- npsp-0.5-3/npsp/R/zzz.R | 2 npsp-0.5-3/npsp/README.md |only npsp-0.5-3/npsp/demo/aquifer.R | 2 npsp-0.5-3/npsp/inst/TODO | 54 - npsp-0.5-3/npsp/man/aquifer.Rd | 91 +- npsp-0.5-3/npsp/man/bin.den.Rd | 99 +- npsp-0.5-3/npsp/man/binning.Rd | 179 ++-- npsp-0.5-3/npsp/man/coords.Rd | 62 - npsp-0.5-3/npsp/man/coordvalues.Rd | 58 - npsp-0.5-3/npsp/man/covar.Rd | 72 - npsp-0.5-3/npsp/man/cpu.time.Rd | 99 +- npsp-0.5-3/npsp/man/data.grid.Rd | 69 - npsp-0.5-3/npsp/man/disc.sb.Rd | 111 +-- npsp-0.5-3/npsp/man/earthquakes.Rd | 77 +- npsp-0.5-3/npsp/man/fitsvar.sb.iso.Rd | 236 +++--- npsp-0.5-3/npsp/man/grid.par.Rd | 90 +- npsp-0.5-3/npsp/man/h.cv.Rd | 284 +++---- npsp-0.5-3/npsp/man/interp.Rd | 132 +-- npsp-0.5-3/npsp/man/kappasb.Rd | 91 +- npsp-0.5-3/npsp/man/locpol.Rd | 307 +++----- npsp-0.5-3/npsp/man/mask.Rd |only npsp-0.5-3/npsp/man/np.den.Rd | 199 ++--- npsp-0.5-3/npsp/man/np.svar.Rd | 307 +++----- npsp-0.5-3/npsp/man/npsp-geoR.Rd | 98 +- npsp-0.5-3/npsp/man/npsp-gstat.Rd | 111 +-- npsp-0.5-3/npsp/man/npsp-internals.Rd | 107 +- npsp-0.5-3/npsp/man/npsp-package.Rd | 185 ++--- npsp-0.5-3/npsp/man/npsp.tolerance.Rd |only npsp-0.5-3/npsp/man/rgraphics.Rd | 151 +--- npsp-0.5-3/npsp/man/rule.Rd |only npsp-0.5-3/npsp/man/simage.Rd | 362 ++++----- npsp-0.5-3/npsp/man/spersp.Rd | 377 ++++------ npsp-0.5-3/npsp/man/splot.Rd | 350 ++++----- npsp-0.5-3/npsp/man/spoints.Rd | 303 +++----- npsp-0.5-3/npsp/man/sv.Rd | 69 - npsp-0.5-3/npsp/man/svar.bin.Rd | 140 +-- npsp-0.5-3/npsp/man/svar.plot.Rd | 120 +-- npsp-0.5-3/npsp/man/svarmod.Rd | 144 +-- npsp-0.5-3/npsp/man/varcov.Rd | 81 +- npsp-0.5-3/npsp/src/Makevars | 11 npsp-0.5-3/npsp/src/besselzeros.f90 | 216 ----- npsp-0.5-3/npsp/src/dsytrfi.f90 | 9 npsp-0.5-3/npsp/src/grid_module.f90 | 40 - npsp-0.5-3/npsp/src/linreg_module.f90 | 12 npsp-0.5-3/npsp/src/lp_module.f90 | 1254 +++++++++++++++++----------------- npsp-0.5-3/npsp/src/svar_module.f90 | 18 npsp-0.5-3/npsp/src/tql2.f |only 77 files changed, 4530 insertions(+), 4723 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences.
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>
Diff between NNS versions 0.2.1 dated 2016-09-13 and 0.2.2 dated 2016-09-29
DESCRIPTION | 8 +-- MD5 | 34 +++++++------- NAMESPACE | 1 R/Classifier.R | 26 +++++------ R/Feature_probability.R | 102 +++++++++++++++++++++++++++++++++++++++----- R/Find_Interval.R | 4 - R/Multivariate_Regression.R | 102 +++++++++++++++++++------------------------- R/Partial_Moments.R | 12 ++--- R/Partition_Map.R | 33 ++++++++------ R/Regression.R | 36 ++++++++------- R/dy_d_wrt.R |only R/dy_dx.R | 27 ++++++++++- man/Feature.probability.Rd | 14 ++++-- man/VN.M.reg.Rd | 6 +- man/VN.class.Rd | 6 +- man/VN.reg.Rd | 6 +- man/dy.d_.Rd |only man/dy.dx.Rd | 9 +++ man/partition.map.Rd | 11 +++- 19 files changed, 283 insertions(+), 154 deletions(-)
Title: Meta-Analysis of Gene Expression Data
Description: A pipeline for the meta-analysis of gene expression data. We have
assembled several analysis and plot functions to
perform integrated multi-cohort analysis of gene expression data (meta-
analysis). Methodology described in:
<http://biorxiv.org/content/early/2016/08/25/071514>.
Author: Winston A. Haynes, Francesco Vallania, Aurelie Tomczak, Timothy Sweeney,
Erika Bongen, Purvesh Khatri
Maintainer: Winston A. Haynes <hayneswa@stanford.edu>
Diff between MetaIntegrator versions 1.0.1 dated 2016-08-30 and 1.0.3 dated 2016-09-29
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/getSampleLevelGeneData.R | 8 ++++++-- inst/doc/MetaIntegrator.Rmd | 4 ++-- inst/doc/MetaIntegrator.html | 14 +++++++------- vignettes/MetaIntegrator.Rmd | 4 ++-- 6 files changed, 27 insertions(+), 23 deletions(-)
More information about MetaIntegrator at CRAN
Permanent link
Title: Bayesian Factor Analysis
Description: Provides model fitting for
several Bayesian factor models including Gaussian,
ordinal probit, mixed and semiparametric Gaussian
copula factor models under a range of priors.
Author: Jared Murray
Maintainer: Jared Murray <jsmurray@stat.cmu.edu>
Diff between bfa versions 0.3.1 dated 2014-02-11 and 0.4 dated 2016-09-29
bfa-0.3.1/bfa/man/corr_samp.Rd |only bfa-0.4/bfa/DESCRIPTION | 19 ++--- bfa-0.4/bfa/MD5 | 78 ++++++++++---------- bfa-0.4/bfa/NAMESPACE | 23 +++++- bfa-0.4/bfa/NEWS | 25 ++++++ bfa-0.4/bfa/R/bfa-package.R | 9 +- bfa-0.4/bfa/R/bfa_copula.R | 23 +++--- bfa-0.4/bfa/R/bfa_gauss.R | 22 ++++- bfa-0.4/bfa/R/bfa_mixed.R | 21 +++-- bfa-0.4/bfa/R/class.R | 24 +++--- bfa-0.4/bfa/R/get_coda.R | 6 + bfa-0.4/bfa/R/main.R | 14 ++- bfa-0.4/bfa/R/plots.R | 2 bfa-0.4/bfa/R/postproc.R | 43 ++++++++++- bfa-0.4/bfa/R/ratings08.R | 2 bfa-0.4/bfa/man/HPDinterval.bfa.Rd | 18 ++-- bfa-0.4/bfa/man/bfa-package.Rd | 22 +++-- bfa-0.4/bfa/man/bfa_copula.Rd | 114 +++++++++++------------------- bfa-0.4/bfa/man/bfa_gauss.Rd | 91 +++++++++++------------ bfa-0.4/bfa/man/bfa_mixed.Rd | 111 ++++++++++++----------------- bfa-0.4/bfa/man/bfa_model.Rd | 39 ++++------ bfa-0.4/bfa/man/biplot.bfa.Rd | 12 +-- bfa-0.4/bfa/man/coef.bfa.Rd | 22 ++--- bfa-0.4/bfa/man/cor_samp.Rd |only bfa-0.4/bfa/man/cov_samp.Rd | 7 + bfa-0.4/bfa/man/get_coda.Rd | 24 ++---- bfa-0.4/bfa/man/get_posterior_loadings.Rd |only bfa-0.4/bfa/man/get_posterior_scores.Rd |only bfa-0.4/bfa/man/mean.bfa.Rd | 13 ++- bfa-0.4/bfa/man/predict.bfa.Rd | 37 ++++----- bfa-0.4/bfa/man/print.bfa.Rd | 6 + bfa-0.4/bfa/man/ratings08.Rd | 14 +-- bfa-0.4/bfa/man/utri_restrict.Rd | 11 +- bfa-0.4/bfa/man/var.bfa.Rd | 17 ++-- bfa-0.4/bfa/man/woodbury.Rd | 6 + bfa-0.4/bfa/src/bfa_common.cpp | 4 - bfa-0.4/bfa/src/bfa_common.h | 17 ++++ bfa-0.4/bfa/src/erl.cpp | 4 - bfa-0.4/bfa/src/imh.cpp | 4 - bfa-0.4/bfa/src/loadings.cpp | 8 +- bfa-0.4/bfa/src/main_mcmc.cpp | 74 +++++++++++++++++-- bfa-0.4/bfa/src/scores.cpp | 4 - 42 files changed, 573 insertions(+), 417 deletions(-)