Title: Compressive Sampling: Sparse Signal Recovery Utilities
Description: Utilities for sparse signal recovery suitable for compressed sensing. L1, L2 and TV penalties, DFT basis matrix, simple sparse signal generator, mutual cumulative coherence between two matrices and examples, Lp complex norm, scaling back regression coefficients.
Author: Mehmet Suzen [aut, cre]
Maintainer: Mehmet Suzen
Diff between R1magic versions 0.2 dated 2013-04-09 and 0.3.2 dated 2015-04-19
R1magic-0.2/R1magic/examples |only R1magic-0.3.2/R1magic/DESCRIPTION | 20 ++++++------ R1magic-0.3.2/R1magic/MD5 | 21 ++++++++----- R1magic-0.3.2/R1magic/NEWS |only R1magic-0.3.2/R1magic/R/Lnorm.R |only R1magic-0.3.2/R1magic/R/objectiveL1.R | 14 ++++++++ R1magic-0.3.2/R1magic/R/objectiveL2.R | 18 ++++++++--- R1magic-0.3.2/R1magic/R/scaleBack.lm.R |only R1magic-0.3.2/R1magic/README.md | 6 +++ R1magic-0.3.2/R1magic/inst |only R1magic-0.3.2/R1magic/man/Lnorm.Rd |only R1magic-0.3.2/R1magic/man/R1magic-package.Rd | 6 +-- R1magic-0.3.2/R1magic/man/objectiveL1.Rd | 43 ++++++++++----------------- R1magic-0.3.2/R1magic/man/objectiveL2.Rd | 43 ++++++++++----------------- R1magic-0.3.2/R1magic/man/scaleBack.lm.Rd |only 15 files changed, 92 insertions(+), 79 deletions(-)
Title: A Bayesian Nonparametric Algorithm for Time Series Clustering
Description: Performs the algorithm for time series clustering described in Nieto-Barajas and Contreras-Cristan (2014).
Author: Martell-Juarez, D.A. & Nieto-Barajas, L.E.
Maintainer: David Alejandro Martell Juarez
Diff between BNPTSclust versions 1.0 dated 2015-01-13 and 1.1 dated 2015-04-19
BNPTSclust-1.0/BNPTSclust/R/readscaleperiods.R |only BNPTSclust-1.0/BNPTSclust/inst/doc/BNPTSclust.pdf |only BNPTSclust-1.0/BNPTSclust/man/readscaleperiods.Rd |only BNPTSclust-1.0/BNPTSclust/vignettes/BNPTSclust.pdf |only BNPTSclust-1.1/BNPTSclust/DESCRIPTION | 8 BNPTSclust-1.1/BNPTSclust/MD5 | 58 - BNPTSclust-1.1/BNPTSclust/R/clusterplots.R |only BNPTSclust-1.1/BNPTSclust/R/comp11.R | 3 BNPTSclust-1.1/BNPTSclust/R/designmatrices.R |only BNPTSclust-1.1/BNPTSclust/R/diagplots.R |only BNPTSclust-1.1/BNPTSclust/R/scaleandperiods.R |only BNPTSclust-1.1/BNPTSclust/R/tseriesca.R | 800 +++++++++------ BNPTSclust-1.1/BNPTSclust/R/tseriescm.R | 925 ++++++++++------- BNPTSclust-1.1/BNPTSclust/R/tseriescq.R | 929 ++++++++++-------- BNPTSclust-1.1/BNPTSclust/data/gdp.rda |binary BNPTSclust-1.1/BNPTSclust/data/houses.rda |binary BNPTSclust-1.1/BNPTSclust/data/stocks.rda |binary BNPTSclust-1.1/BNPTSclust/data/tseriesca.out.rda |binary BNPTSclust-1.1/BNPTSclust/data/tseriescm.out.rda |binary BNPTSclust-1.1/BNPTSclust/data/tseriescq.out.rda |binary BNPTSclust-1.1/BNPTSclust/inst/doc/BNPTSclust1.1.pdf |only BNPTSclust-1.1/BNPTSclust/man/BNPTSclust-package.Rd | 17 BNPTSclust-1.1/BNPTSclust/man/clusterplots.Rd |only BNPTSclust-1.1/BNPTSclust/man/comp11.Rd | 28 BNPTSclust-1.1/BNPTSclust/man/designmatrices.Rd |only BNPTSclust-1.1/BNPTSclust/man/diagplots.Rd |only BNPTSclust-1.1/BNPTSclust/man/gdp.Rd | 2 BNPTSclust-1.1/BNPTSclust/man/houses.Rd | 4 BNPTSclust-1.1/BNPTSclust/man/scaleandperiods.Rd |only BNPTSclust-1.1/BNPTSclust/man/stocks.Rd | 2 BNPTSclust-1.1/BNPTSclust/man/tseriesca.Rd | 228 +--- BNPTSclust-1.1/BNPTSclust/man/tseriesca.out.Rd | 4 BNPTSclust-1.1/BNPTSclust/man/tseriescm.Rd | 222 +--- BNPTSclust-1.1/BNPTSclust/man/tseriescm.out.Rd | 4 BNPTSclust-1.1/BNPTSclust/man/tseriescq.Rd | 217 +--- BNPTSclust-1.1/BNPTSclust/man/tseriescq.out.Rd | 4 BNPTSclust-1.1/BNPTSclust/vignettes/BNPTSclust1.1.pdf |only 37 files changed, 1821 insertions(+), 1634 deletions(-)
Title: "Hit and Run" and "Shake and Bake" for Sampling Uniformly from
Convex Shapes
Description: The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints.
Author: Gert van Valkenhoef, Tommi Tervonen
Maintainer: Gert van Valkenhoef
Diff between hitandrun versions 0.5 dated 2015-01-06 and 0.5-1 dated 2015-04-19
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS | 11 +++++++++-- R/bound.R | 10 +++++++++- 4 files changed, 26 insertions(+), 11 deletions(-)
Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel regression based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently computes SNP-set level p-values, while adjusting for covariates.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee
Diff between SKAT versions 1.0.1 dated 2014-11-04 and 1.0.7 dated 2015-04-19
SKAT-1.0.1/SKAT/R/KMTest_Linear.R |only SKAT-1.0.1/SKAT/R/KMTest_Logistic.R |only SKAT-1.0.1/SKAT/R/KMTest_Logistic_VarMatching.R |only SKAT-1.0.1/SKAT/R/KMTest_Optimal.R |only SKAT-1.0.1/SKAT/R/KMTest_Optimal_VarMatching.R |only SKAT-1.0.1/SKAT/src/NPsort.cpp |only SKAT-1.0.7/SKAT/DESCRIPTION | 12 - SKAT-1.0.7/SKAT/MD5 | 59 +++--- SKAT-1.0.7/SKAT/NAMESPACE | 3 SKAT-1.0.7/SKAT/R/Binary_Function.R | 45 +++- SKAT-1.0.7/SKAT/R/Binary_MAIN.R | 43 +++- SKAT-1.0.7/SKAT/R/Binary_MAIN_ExactBin.R | 230 ++++++++++++++++++------ SKAT-1.0.7/SKAT/R/Function.R | 37 +++ SKAT-1.0.7/SKAT/R/Function_Power_Resampling.R | 2 SKAT-1.0.7/SKAT/R/Main.R | 142 ++++++++++---- SKAT-1.0.7/SKAT/R/Null_Model.R | 18 + SKAT-1.0.7/SKAT/R/SKAT_Linear.R |only SKAT-1.0.7/SKAT/R/SKAT_Logistic.R |only SKAT-1.0.7/SKAT/R/SKAT_Logistic_VarMatching.R |only SKAT-1.0.7/SKAT/R/SKAT_Optimal.R |only SKAT-1.0.7/SKAT/R/SKAT_Optimal_VarMatching.R |only SKAT-1.0.7/SKAT/R/X_Chrom.R |only SKAT-1.0.7/SKAT/data/SKAT.example.ChrX.rda |only SKAT-1.0.7/SKAT/data/datalist | 3 SKAT-1.0.7/SKAT/inst/doc/SKAT.pdf |binary SKAT-1.0.7/SKAT/man/Get_EffectiveNumberTest.rd | 2 SKAT-1.0.7/SKAT/man/SKAT.example.ChrX.rd |only SKAT-1.0.7/SKAT/man/SKAT_ChrX.rd |only SKAT-1.0.7/SKAT/man/SKAT_Null_Model.rd | 7 SKAT-1.0.7/SKAT/src/Binary_global.cpp | 2 SKAT-1.0.7/SKAT/src/NPsort.h | 46 ++++ SKAT-1.0.7/SKAT/src/bed_reader.cpp | 70 +++---- SKAT-1.0.7/SKAT/src/bed_reader.h | 20 +- SKAT-1.0.7/SKAT/src/interface_to_R.cpp | 6 SKAT-1.0.7/SKAT/src/mwo_reader.cpp | 67 +++--- SKAT-1.0.7/SKAT/src/mwo_reader.h | 27 +- SKAT-1.0.7/SKAT/src/setid_bim_index.cpp | 40 ++-- SKAT-1.0.7/SKAT/src/setid_bim_index.h | 12 - 38 files changed, 625 insertions(+), 268 deletions(-)
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Title: Tools for Phoneticians and Phonologists
Description: Tools for phoneticians and phonologists, including functions for normalization and plotting of vowels.
Author: Daniel R. McCloy
Maintainer: Daniel R. McCloy
Diff between phonR versions 1.0-1 dated 2015-03-05 and 1.0-3 dated 2015-04-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/phonR.R | 21 +++++++++++---------- 3 files changed, 17 insertions(+), 16 deletions(-)
Title: Tools for Analyzing Finite Mixture Models
Description: A collection of R functions for analyzing finite mixture models. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.
Author: Derek Young [aut, cre],
Tatiana Benaglia [aut],
Didier Chauveau [aut],
David Hunter [aut],
Ryan Elmore [ctb],
Thomas Hettmansperger [ctb],
Hoben Thomas [ctb],
Fengjuan Xuan [ctb]
Maintainer: Derek Young
Diff between mixtools versions 1.0.2 dated 2014-05-14 and 1.0.3 dated 2015-04-19
DESCRIPTION | 16 - MD5 | 51 ++-- NAMESPACE | 17 + NEWS | 13 + R/multmixEM.R | 9 R/npMSL.R | 486 ++++++++++++++++++++++++++++++--------------- build |only inst/doc/mixtools.R | 10 inst/doc/mixtools.Rnw | 23 +- inst/doc/mixtools.pdf |binary man/ise.npEM.Rd | 221 ++++++++++---------- man/mixtools-internal.Rd | 41 +++ man/npEM.Rd | 24 +- man/npMSL.Rd | 61 +++-- man/plot.npEM.Rd | 4 man/plotFDR.Rd | 4 man/print.npEM.Rd | 2 man/regmixEM.Rd | 3 man/regmixEM.mixed.Rd | 5 man/repnormmixEM.Rd | 2 man/repnormmixmodel.sel.Rd | 2 man/spEMsymlocN01.Rd | 9 man/summary.npEM.Rd | 4 man/wkde.Rd | 124 +++++------ src/npMSL.c | 54 ++--- vignettes/mixtools.Rnw | 23 +- vignettes/mixtools.bib | 9 27 files changed, 761 insertions(+), 456 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian framework. You need either BUGS or JAGS to use this package, preferably JAGS (through the rjags package). Includes methods to assess heterogeneity and inconsistency, and a number of standard visualizations.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef
Diff between gemtc versions 0.6-1 dated 2014-12-12 and 0.6-2 dated 2015-04-19
DESCRIPTION | 11 +- MD5 | 18 +-- NAMESPACE | 3 NEWS | 20 +++ R/anohe.R | 6 - R/blobbogram.R | 45 +++++--- R/inits.R | 7 + R/mtc.network.R | 92 ++++++++++++------ man/blobbogram.Rd | 10 + tests/testthat/test-unit-mtc.nr.comparisons.R |only tests/testthat/test-unit-mtc.study.treatment.matrix.R |only 11 files changed, 145 insertions(+), 67 deletions(-)
Title: Models for Skewed Count Distributions Relevant to Networks
Description: Likelihood-based inference for skewed count distributions used in network modeling. "degreenet" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock
Maintainer: Mark S. Handcock
Diff between degreenet versions 1.3 dated 2015-04-06 and 1.3-1 dated 2015-04-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/cmp.R | 39 +++++++++++++++++++++++++++++---------- R/degreenet.R | 2 +- src/cmp.c | 48 +++++++++++++++++++++++++++++++++++++----------- src/cmp.h | 2 +- 6 files changed, 77 insertions(+), 32 deletions(-)
Title: Visualizing Generalized Canonical Discriminant and Canonical
Correlation Analysis
Description: Functions for computing and visualizing
generalized canonical discriminant analyses and canonical correlation analysis
for a multivariate linear model.
Traditional canonical discriminant analysis is restricted to a one-way 'MANOVA'
design and is equivalent to canonical correlation analysis between a set of quantitative
response variables and a set of dummy variables coded from the factor variable.
The 'candisc' package generalizes this to higher-way 'MANOVA' designs
for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The graphic functions provide low-rank (1D, 2D, 3D)
visualizations of terms in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Related plots are
now provided for canonical correlation analysis when all predictors are quantitative.
Author: Michael Friendly [aut, cre], John Fox [aut]
Maintainer: Michael Friendly
Diff between candisc versions 0.6-5 dated 2013-06-12 and 0.6-7 dated 2015-04-19
DESCRIPTION | 44 ++++++------- MD5 | 33 +++++----- NAMESPACE | 5 + NEWS | 157 ++++++++++++++++++++++++++----------------------- R/can_lm.R |only R/heplot.candisc.R | 42 ++++++------- R/heplot3d.cancor.R | 9 +- R/mlm2can.R |only R/plot.candisc.R | 10 +-- R/vecscale.R |only R/vectors3d.R | 4 - data/Grass.rda |binary data/HSB.rda |binary data/Wolves.rda |binary man/HSB.Rd | 4 - man/can_lm.Rd |only man/candisc-package.Rd | 4 - man/candisc.Rd | 4 - man/heplot.candisc.Rd | 6 - man/vecscale.Rd |only 20 files changed, 173 insertions(+), 149 deletions(-)
Title: Graph Estimation Based on Birth-Death MCMC Approach
Description: A general framework to perform Bayesian structure learning in undirected graphical models. The main target is high-dimensional data analysis wherein either continuous or discrete variables.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi
Diff between BDgraph versions 2.17 dated 2015-03-10 and 2.18 dated 2015-04-19
BDgraph-2.17/BDgraph/DESCRIPTION |only BDgraph-2.17/BDgraph/MD5 |only BDgraph-2.17/BDgraph/NAMESPACE |only BDgraph-2.17/BDgraph/R |only BDgraph-2.17/BDgraph/build |only BDgraph-2.17/BDgraph/data |only BDgraph-2.17/BDgraph/man |only BDgraph-2.17/BDgraph/src |only BDgraph-2.17/BDgraph/vignettes |only BDgraph-2.18/BDgraph/inst/doc/BDgraph.pdf |binary BDgraph-2.18/BDgraph/inst/doc/vignette.pdf |binary 11 files changed