Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data.
Functions are provided to rapidly read from and write to VCF files.
Once VCF data is read into R a parser function extracts matrices of data.
This information can then be used for quality control or other purposes.
Additional functions provide visualization of genomic data.
Once processing is complete data may be written to a VCF file (*.vcf.gz).
It also may be converted into other popular R objects (e.g., genlight, DNAbin).
VcfR provides a link between VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut],
Niklaus J. Grunwald [aut],
Eric C. Anderson [ctb],
David J. Winter [ctb]
Maintainer: Brian J. Knaus <briank.lists@gmail.com>
Diff between vcfR versions 1.1.0 dated 2016-05-26 and 1.2.0 dated 2016-07-25
DESCRIPTION | 6 - MD5 | 95 ++++++++++---------- NAMESPACE | 1 R/AllClass.R | 4 R/RcppExports.R | 10 ++ R/addID.R | 18 ++- R/chromo_plot.R | 3 R/create_chromR.R | 2 R/extract_gt.R | 21 ++-- R/heatmap_bp.R | 13 +- R/io_vcfR.R | 10 +- R/vcfR_conversion.R | 5 + R/vcfR_to_tidy_functions.R | 90 ++++++++++++++----- README.md | 35 +++++-- inst/CITATION | 7 - inst/doc/converting_data.R | 5 + inst/doc/converting_data.Rmd | 15 +++ inst/doc/converting_data.html | 153 ++++++++++++++++++++++---------- inst/doc/filtering_data.html | 138 ++++++++++++++++------------- inst/doc/intro_to_vcfR.Rmd | 6 - inst/doc/intro_to_vcfR.html | 108 +++++++++++++--------- inst/doc/ranking_data.html | 174 ++++++++++++++++++++----------------- inst/doc/sequence_coverage.R | 5 + inst/doc/sequence_coverage.Rmd | 13 ++ inst/doc/sequence_coverage.html | 120 ++++++++++++++++--------- inst/doc/vcf_data.R | 6 - inst/doc/vcf_data.Rmd | 6 - inst/doc/vcf_data.html | 65 ++++++++----- inst/doc/visualization_1.html | 136 ++++++++++++++++------------ inst/doc/visualization_2.Rmd | 2 inst/doc/visualization_2.html | 126 +++++++++++++++----------- man/addID.Rd | 14 ++ man/chromR-class.Rd | 4 man/create_chromR.Rd | 2 man/io_vcfR.Rd | 3 man/is_het.Rd | 7 + man/vcfR_to_tidy_conversion.Rd | 7 + src/RcppExports.cpp | 12 ++ src/is_het.cpp |only src/vcfRCommon.cpp | 47 +++++++++ src/vcfRCommon.h | 3 tests/testthat.R | 2 tests/testthat/test_1_vcf.R | 97 ++++++++++++++++++++ tests/testthat/test_3_extract_gt.R | 12 ++ tests/testthat/test_heatmapbp.R | 9 + tests/testthat/test_is_het.R | 52 +++++++++++ tests/testthat/test_vcfRtidy.R | 26 +++++ vignettes/intro_to_vcfR.Rmd | 6 - vignettes/visualization_2.Rmd | 2 49 files changed, 1157 insertions(+), 546 deletions(-)
Title: Learning Principal Graphs with DDRTree
Description: Project data into a reduced dimensional space and construct a principal graph from the reduced dimension.
Author: Xiaojie Qiu, Cole Trapnell, Qi Mao, Li Wang
Maintainer: Xiaojie Qiu <xqiu@uw.edu>
Diff between DDRTree versions 0.1.3 dated 2016-02-02 and 0.1.4 dated 2016-07-25
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/DDRTree.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui <fhui28@gmail.com>
Diff between boral versions 1.0 dated 2016-06-17 and 1.0.1 dated 2016-07-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/auxilaryfunctions.R | 4 ++-- R/boral.jags.R | 5 ++++- inst/NEWS.Rd | 5 ++++- 5 files changed, 18 insertions(+), 12 deletions(-)
Title: Variance Component Analysis
Description:
ANOVA and REML estimation of linear mixed models is implemented, once following
Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package.
The primary objective of this package is to perform a variance component analysis (VCA)
according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement
Procedures" (2014). There are plotting methods for visualization of an experimental design,
plotting random effects and residuals. For ANOVA type estimation two methods for computing
ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of
variance components can be derived, which is used in estimating confidence intervals. Linear
hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific
values of covariables and with custom weighting schemes for factor variables. See ?VCA for a
more comprehensive description of the features.
Author: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VCA versions 1.3.1 dated 2016-04-04 and 1.3.2 dated 2016-07-25
DESCRIPTION | 10 MD5 | 128 ++++----- NAMESPACE | 7 R/plot.R | 250 ++++++++++++++++-- R/vca.R | 534 +++++++++++++++++++++++++++++++--------- inst/ChangeLog.txt | 29 ++ inst/UnitTests/runit.anovaMM.R | 16 + inst/UnitTests/runit.anovaVCA.R | 13 inst/UnitTests/runit.misc.R | 152 +++++++++++ inst/UnitTests/runit.remlMM.R | 137 +++++++--- inst/UnitTests/runit.remlVCA.R | 77 ++++- man/Csweep.Rd | 38 ++ man/DfSattHelper.Rd | 4 man/MPinv.Rd | 10 man/SattDF.Rd | 13 man/Sinv.Rd | 21 + man/Solve.Rd | 8 man/Trace.Rd | 4 man/VCA-Package.Rd | 27 +- man/VCAinference.Rd | 64 ++-- man/anovaDF.Rd | 15 - man/anovaMM.Rd | 48 +-- man/anovaVCA.Rd | 50 +-- man/as.matrix.VCA.Rd | 8 man/as.matrix.VCAinference.Rd |only man/buildList.Rd | 15 - man/check4MKL.Rd | 2 man/coef.VCA.Rd | 6 man/fixef.Rd | 2 man/fixef.VCA.Rd | 14 - man/getAmatrix.Rd | 2 man/getCmatrix.Rd | 16 - man/getDDFM.Rd | 6 man/getDF.Rd | 4 man/getGB.Rd | 12 man/getL.Rd | 10 man/getMM.Rd | 11 man/getMat.Rd | 13 man/getSSQqf.Rd | 6 man/getSSQsweep.Rd | 10 man/getV.Rd | 4 man/getVCvar.Rd | 4 man/isBalanced.Rd | 19 - man/lmerG.Rd | 21 + man/lmerMatrices.Rd | 10 man/lmerSummary.Rd | 43 ++- man/load_if_installed.Rd | 4 man/lsmMat.Rd | 6 man/lsmeans.Rd | 20 - man/plot.VCA.Rd |only man/plotRandVar.Rd | 19 - man/print.VCA.Rd | 4 man/print.VCAinference.Rd | 7 man/ranef.Rd | 2 man/ranef.VCA.Rd | 12 man/remlMM.Rd | 47 +-- man/remlVCA.Rd | 20 - man/residuals.VCA.Rd | 23 - man/solveMME.Rd | 12 man/stepwiseVCA.Rd | 12 man/test.fixef.Rd | 24 - man/test.lsmeans.Rd | 16 - man/varPlot.Rd | 146 ++++++---- man/vcov.VCA.Rd | 2 man/vcovFixed.Rd | 4 man/vcovVC.Rd | 8 66 files changed, 1614 insertions(+), 667 deletions(-)
Title: Treatment Effect eXplorer for Microbial Ecology eXperiments
(using Sequence Counts)
Description: Analysis and visualization of community dynamics in microbial
ecology experiments (that use sequence count data) using the
truncated Poisson lognormal distribution.
Author: Scott Olesen
Maintainer: Scott Olesen <swo@mit.edu>
Diff between texmexseq versions 0.2 dated 2016-05-26 and 0.3 dated 2016-07-25
DESCRIPTION | 11 ++++++----- MD5 | 12 ++++++------ NAMESPACE | 3 ++- R/session.R | 14 ++++++-------- README.md | 3 +++ demo/demo.R | 2 +- man/z-transform-sample.Rd | 23 ++++++++++++++--------- 7 files changed, 38 insertions(+), 30 deletions(-)
Title: Interface Utilities, Model Templates, Parallel Computing Methods
and Additional Distributions for MCMC Models in JAGS
Description: User-friendly interface utilities for MCMC models via
Just Another Gibbs Sampler (JAGS), facilitating the use of parallel
(or distributed) processors for multiple chains, automated control
of convergence and sample length diagnostics, and evaluation of the
performance of a model using drop-k validation or against simulated
data. Template model specifications can be generated using a standard
lme4-style formula interface to assist users less familiar with the
BUGS syntax. A JAGS extension module provides additional distributions
including the Pareto family of distributions, the DuMouchel prior and
the half-Cauchy prior.
Author: Matthew Denwood [aut, cre],
Martyn Plummer [cph] (Copyright holder of the code in
/src/distributions/jags, src/distributions/DPar1.*, configure.ac,
and original copyright holder of some modified code where
indicated)
Maintainer: Matthew Denwood <md@sund.ku.dk>
Diff between runjags versions 2.0.3-2 dated 2016-03-31 and 2.0.4-2 dated 2016-07-25
runjags-2.0.3-2/runjags/inst/doc/userguide.Rtex |only runjags-2.0.3-2/runjags/inst/doc/userguide.pdf |only runjags-2.0.3-2/runjags/vignettes/userguide.Rtex |only runjags-2.0.4-2/runjags/CHANGELOG | 29 ++++ runjags-2.0.4-2/runjags/DESCRIPTION | 29 ++-- runjags-2.0.4-2/runjags/MD5 | 72 +++++------ runjags-2.0.4-2/runjags/R/autoextend.jags.R | 8 - runjags-2.0.4-2/runjags/R/dump.list.format.R | 2 runjags-2.0.4-2/runjags/R/extend.jags.R | 4 runjags-2.0.4-2/runjags/R/extract.runjags.R | 4 runjags-2.0.4-2/runjags/R/mutate.functions.R | 4 runjags-2.0.4-2/runjags/R/print.methods.R | 2 runjags-2.0.4-2/runjags/R/read.jagsfile.R | 6 runjags-2.0.4-2/runjags/R/runjags.start.R | 27 +++- runjags-2.0.4-2/runjags/R/runjags.summaries.R | 2 runjags-2.0.4-2/runjags/R/summary.R | 19 ++ runjags-2.0.4-2/runjags/R/template.jags.R | 22 ++- runjags-2.0.4-2/runjags/R/utilities.R | 18 ++ runjags-2.0.4-2/runjags/R/utilities.invisible.R | 4 runjags-2.0.4-2/runjags/build/vignette.rds |binary runjags-2.0.4-2/runjags/inst/CITATION | 36 ++--- runjags-2.0.4-2/runjags/inst/doc/UserGuide.Rtex |only runjags-2.0.4-2/runjags/inst/doc/UserGuide.pdf |only runjags-2.0.4-2/runjags/inst/doc/quickjags.html | 127 ++++++++++---------- runjags-2.0.4-2/runjags/man/add.summary.Rd | 20 ++- runjags-2.0.4-2/runjags/man/autorun.jags.Rd | 12 + runjags-2.0.4-2/runjags/man/combine.mcmc.Rd | 2 runjags-2.0.4-2/runjags/man/extract.runjags.Rd | 2 runjags-2.0.4-2/runjags/man/mutate.functions.Rd | 5 runjags-2.0.4-2/runjags/man/read.jagsfile.Rd | 7 - runjags-2.0.4-2/runjags/man/results.jags.Rd | 12 - runjags-2.0.4-2/runjags/man/run.jags.Rd | 33 ++--- runjags-2.0.4-2/runjags/man/run.jags.study.Rd | 2 runjags-2.0.4-2/runjags/man/runjags-class.Rd | 2 runjags-2.0.4-2/runjags/man/runjags.printmethods.Rd | 5 runjags-2.0.4-2/runjags/man/template.jags.Rd | 6 runjags-2.0.4-2/runjags/man/testjags.Rd | 3 runjags-2.0.4-2/runjags/man/write.jagsfile.Rd | 18 +- runjags-2.0.4-2/runjags/vignettes/UserGuide.Rtex |only runjags-2.0.4-2/runjags/vignettes/traceplots.pdf |binary 40 files changed, 338 insertions(+), 206 deletions(-)
Title: Sample Size Calculations for Longitudinal Data
Description: The longpower package contains functions for computing
power and sample size for linear models of longitudinal data
based on the formula due to Liu and Liang (1997) and Diggle et
al (2002). Either formula is expressed in terms of marginal
model or Generalized Estimating Equations (GEE) parameters.
This package contains functions which translate pilot mixed
effect model parameters (e.g. random intercept and/or slope)
into marginal model parameters so that the formulas of Diggle
et al or Liu and Liang formula can be applied to produce sample
size calculations for two sample longitudinal designs assuming
known variance.
Author: Michael C. Donohue, Anthony C. Gamst, Steven D. Edland
Maintainer: Michael C. Donohue <mdonohue@usc.edu>
Diff between longpower versions 1.0-15 dated 2016-05-17 and 1.0-16 dated 2016-07-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/longpower.pdf |binary tests/testthat/tests.R | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Toolkit for Item Factor Analysis with OpenMx
Description: Tools, tutorials, and demos of Item Factor Analysis using OpenMx.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between ifaTools versions 0.10 dated 2016-05-16 and 0.11 dated 2016-07-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/doc/pritikin-schmidt.R | 2 +- inst/doc/pritikin-schmidt.Rnw | 2 +- inst/doc/pritikin-schmidt.pdf |binary inst/modelBuilder/server.R | 2 +- vignettes/pritikin-schmidt.Rnw | 2 +- 8 files changed, 15 insertions(+), 15 deletions(-)
Title: Conversion Tools for HK80 Geographical Coordinate System
Description: This is a collection of functions for converting coordinates between WGS84UTM, WGS84GEO, HK80UTM, HK80GEO and HK1980GRID Coordinate Systems used in Hong Kong SAR, based on the algorithms described in Explanatory Notes on Geodetic Datums in Hong Kong by Survey and Mapping Office Lands Department, Hong Kong Government (1995).
Author: Jinlong Zhang [aut, cre]
Maintainer: Jinlong Zhang <jinlongzhang01@gmail.com>
Diff between HK80 versions 0.0.1 dated 2014-05-02 and 0.0.2 dated 2016-07-25
DESCRIPTION | 15 +++++---- MD5 | 65 +++++++++++++++++++++--------------------- R/HK1980GRID_TO_HK80GEO.R | 2 - R/HK80GEO_TO_HK1980GRID.R | 2 - R/HK80GEO_TO_HK80UTM.R | 4 +- R/HK80GEO_TO_WGS84GEO.R | 3 + R/HK80UTM_TO_HK80GEO.R | 2 - R/HK80UTM_TO_WGS84UTM.R | 2 - R/WGS84GEO_TO_HK80GEO.R | 3 + R/WGS84GEO_TO_WGS84UTM.R | 2 - R/WGS84UTM_TO_HK80UTM.R | 2 - R/WGS84UTM_TO_WGS84GEO.R | 2 - README.md |only man/HK1980GRID_TO_HK80GEO.Rd | 6 ++- man/HK1980GRID_TO_HK80UTM.Rd | 10 +++--- man/HK1980GRID_TO_WGS84GEO.Rd | 5 +-- man/HK1980GRID_TO_WGS84UTM.Rd | 10 ++++-- man/HK80-package.Rd | 11 +++---- man/HK80GEO_TO_HK1980GRID.Rd | 5 +-- man/HK80GEO_TO_HK80UTM.Rd | 6 ++- man/HK80GEO_TO_WGS84GEO.Rd | 5 +-- man/HK80GEO_TO_WGS84UTM.Rd | 8 +++-- man/HK80UTM_TO_HK1980GRID.Rd | 7 +++- man/HK80UTM_TO_HK80GEO.Rd | 9 +++-- man/HK80UTM_TO_WGS84GEO.Rd | 8 +++-- man/HK80UTM_TO_WGS84UTM.Rd | 5 +-- man/WGS84GEO_TO_HK1980GRID.Rd | 10 +++--- man/WGS84GEO_TO_HK80GEO.Rd | 8 +++-- man/WGS84GEO_TO_HK80UTM.Rd | 8 +++-- man/WGS84GEO_TO_WGS84UTM.Rd | 9 ++--- man/WGS84UTM_TO_HK1980GRID.Rd | 11 +++---- man/WGS84UTM_TO_HK80GEO.Rd | 2 - man/WGS84UTM_TO_HK80UTM.Rd | 9 +++-- man/WGS84UTM_TO_WGS84GEO.Rd | 6 +-- 34 files changed, 151 insertions(+), 111 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects.
7) Multivariate joint frailty models for two types of recurrent events and a terminal event.
8) Joint models for longitudinal data and a terminal event.
9) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available. Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.9.3.1 dated 2016-07-08 and 2.9.4 dated 2016-07-25
frailtypack-2.9.3.1/frailtypack/vignettes/Package_summary.html |only frailtypack-2.9.4/frailtypack/DESCRIPTION | 8 frailtypack-2.9.4/frailtypack/MD5 | 12 frailtypack-2.9.4/frailtypack/NEWS | 6 frailtypack-2.9.4/frailtypack/build |only frailtypack-2.9.4/frailtypack/inst/doc/Package_summary.Rmd | 50 frailtypack-2.9.4/frailtypack/inst/doc/Package_summary.html | 770 ++++------ frailtypack-2.9.4/frailtypack/vignettes/Package_summary.Rmd | 4 8 files changed, 431 insertions(+), 419 deletions(-)
Title: Direct, Chain and Average Equating Coefficients with Standard
Errors Using IRT Methods
Description: Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items. Test scoring can be performed by true score equating and observed score equating methods.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>
Diff between equateIRT versions 2.0 dated 2016-03-30 and 2.0-1 dated 2016-07-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/functions.r | 31 +++++++++++++++++++------------ build/vignette.rds |binary inst/NEWS | 11 ++--------- inst/doc/equateIRT.pdf |binary man/equateIRT-package.Rd | 4 ++-- vignettes/equateIRT.Rnw | 3 +-- 8 files changed, 35 insertions(+), 36 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.1.3.1 dated 2015-07-24 and 1.2.0 dated 2016-07-25
ddalpha-1.1.3.1/ddalpha/R/RcppExports.R |only ddalpha-1.1.3.1/ddalpha/man/nlm_optimize_r.Rd |only ddalpha-1.1.3.1/ddalpha/src/RcppExports.cpp |only ddalpha-1.2.0/ddalpha/DESCRIPTION | 8 ddalpha-1.2.0/ddalpha/MD5 | 116 ++--- ddalpha-1.2.0/ddalpha/NAMESPACE | 7 ddalpha-1.2.0/ddalpha/R/compclassf.r | 2 ddalpha-1.2.0/ddalpha/R/ddalpha-internal.r | 376 +++++++++++------ ddalpha-1.2.0/ddalpha/R/ddalpha.classify.r | 101 +--- ddalpha-1.2.0/ddalpha/R/ddalpha.test.r | 13 ddalpha-1.2.0/ddalpha/R/ddalpha.train.r | 135 ++++-- ddalpha-1.2.0/ddalpha/R/ddalphaf.r | 101 +++- ddalpha-1.2.0/ddalpha/R/ddalphaf.test.r |only ddalpha-1.2.0/ddalpha/R/depth.contours.r | 87 ++- ddalpha-1.2.0/ddalpha/R/depth.halfspace.r | 9 ddalpha-1.2.0/ddalpha/R/depth.projection.r | 18 ddalpha-1.2.0/ddalpha/R/depth.spatial.r | 49 +- ddalpha-1.2.0/ddalpha/R/dknn.R |only ddalpha-1.2.0/ddalpha/R/draw.ddplot.r | 38 + ddalpha-1.2.0/ddalpha/R/knnaff.r | 26 - ddalpha-1.2.0/ddalpha/R/mahalanobis.scaling.r | 28 + ddalpha-1.2.0/ddalpha/R/routines.r | 4 ddalpha-1.2.0/ddalpha/R/separator.polynomial.r | 12 ddalpha-1.2.0/ddalpha/man/CustomMethods.Rd |only ddalpha-1.2.0/ddalpha/man/compclassf.train.Rd | 4 ddalpha-1.2.0/ddalpha/man/dataf.tecator.Rd | 4 ddalpha-1.2.0/ddalpha/man/ddalpha-package.Rd | 11 ddalpha-1.2.0/ddalpha/man/ddalpha.getErrorRateCV.Rd | 2 ddalpha-1.2.0/ddalpha/man/ddalpha.getErrorRatePart.Rd | 9 ddalpha-1.2.0/ddalpha/man/ddalpha.train.Rd | 33 + ddalpha-1.2.0/ddalpha/man/ddalphaf.getErrorRateCV.Rd |only ddalpha-1.2.0/ddalpha/man/ddalphaf.getErrorRatePart.Rd |only ddalpha-1.2.0/ddalpha/man/ddalphaf.test.Rd |only ddalpha-1.2.0/ddalpha/man/ddalphaf.train.Rd | 32 + ddalpha-1.2.0/ddalpha/man/depth.contours.Rd | 6 ddalpha-1.2.0/ddalpha/man/depth.contours.ddalpha.Rd | 9 ddalpha-1.2.0/ddalpha/man/depth.potential.Rd | 2 ddalpha-1.2.0/ddalpha/man/depth.space.spatial.Rd | 7 ddalpha-1.2.0/ddalpha/man/depth.spatial.Rd | 7 ddalpha-1.2.0/ddalpha/man/dknn.classify.Rd |only ddalpha-1.2.0/ddalpha/man/dknn.classify.trained.Rd |only ddalpha-1.2.0/ddalpha/man/dknn.train.Rd |only ddalpha-1.2.0/ddalpha/man/draw.ddplot.Rd | 5 ddalpha-1.2.0/ddalpha/man/getdata.Rd | 7 ddalpha-1.2.0/ddalpha/man/is.in.convex.Rd | 4 ddalpha-1.2.0/ddalpha/src/AlphaProcedure.cpp | 60 ++ ddalpha-1.2.0/ddalpha/src/Common.cpp | 98 +++- ddalpha-1.2.0/ddalpha/src/Common.h | 22 ddalpha-1.2.0/ddalpha/src/DKnn.cpp |only ddalpha-1.2.0/ddalpha/src/DKnn.h |only ddalpha-1.2.0/ddalpha/src/DataStructures.h | 6 ddalpha-1.2.0/ddalpha/src/Knn.cpp | 22 ddalpha-1.2.0/ddalpha/src/Mahalanobis.cpp |only ddalpha-1.2.0/ddalpha/src/Mahalanobis.h |only ddalpha-1.2.0/ddalpha/src/Polynomial.cpp | 282 +++++++----- ddalpha-1.2.0/ddalpha/src/Polynomial.h | 4 ddalpha-1.2.0/ddalpha/src/ProjectionDepth.cpp | 42 - ddalpha-1.2.0/ddalpha/src/ProjectionDepth.h | 8 ddalpha-1.2.0/ddalpha/src/SimplicialDepth.cpp | 59 ++ ddalpha-1.2.0/ddalpha/src/SimplicialDepth.h | 2 ddalpha-1.2.0/ddalpha/src/TukeyDepth.cpp | 86 +-- ddalpha-1.2.0/ddalpha/src/TukeyDepth.h | 6 ddalpha-1.2.0/ddalpha/src/ZonoidDepth.cpp | 32 + ddalpha-1.2.0/ddalpha/src/ZonoidDepth.h | 3 ddalpha-1.2.0/ddalpha/src/asa047.cpp |only ddalpha-1.2.0/ddalpha/src/asa047.h |only ddalpha-1.2.0/ddalpha/src/ddalpha.cpp | 203 +++++---- ddalpha-1.2.0/ddalpha/src/stdafx.h | 9 68 files changed, 1456 insertions(+), 760 deletions(-)
Title: Classification, Regression and Feature Evaluation
Description: This is a suite of machine learning algorithms written in C++ with R
interface. It contains several machine learning model learning techniques in
classification and regression, for example classification and regression trees with
optional constructive induction and models in the leaves, random forests, kNN,
naive Bayes, and locally weighted regression. All predictions obtained with these
models can be explained and visualized with ExplainPrediction package.
The package is especially strong in feature evaluation where it contains several variants of
Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini,
information gain, MDL, and DKM. These methods can be used for example to discretize
numeric attributes.
Its additional feature is OrdEval algorithm and its visualization used for evaluation
of data sets with ordinal features and class, enabling analysis according to the
Kano model of customer satisfaction.
Several algorithms support parallel multithreaded execution via OpenMP.
The top-level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja and Petr Savicky with contributions from John Adeyanju Alao
Maintainer: "Marko Robnik-Sikonja" <marko.robnik@fri.uni-lj.si>
Diff between CORElearn versions 1.47.1 dated 2015-09-04 and 1.48.0 dated 2016-07-25
ChangeLog | 201 +++++++++++++++++----------------- DESCRIPTION | 10 - MD5 | 30 ++--- NAMESPACE | 10 - R/Rinterface.R | 101 +++++++++-------- R/ordEval.R | 66 ++++++----- man/CORElearn-package.Rd | 2 man/ordEval.Rd | 274 +++++++++++++++++++++++------------------------ man/plot.ordEval.Rd | 7 - man/saveRF.Rd | 25 ++-- src/Rfront.cpp | 37 +++--- src/Rfront.h | 3 src/binarize.cpp | 36 +++--- src/binarizeReg.cpp | 34 ++--- src/frontend.cpp | 2 src/rndforest.cpp | 4 16 files changed, 436 insertions(+), 406 deletions(-)
Title: Conditional Formatting in Data Frames
Description: Apply and visualize conditional formatting to data frames in R.
It renders a data frame with cells formatted according to
criteria defined by rules, using a syntax similar to 'ggplot2'. The table is
printed either opening a web browser or within the 'RStudio' viewer if
available. The conditional formatting rules allow to highlight cells
matching a condition or add a gradient background to a given column. This
package supports both 'HTML' and 'LaTeX' outputs in 'knitr' reports, and
exporting to an 'xlsx' file.
Author: Sergio Oller Moreno [aut, cph, cre]
Maintainer: Sergio Oller Moreno <sergioller@gmail.com>
Diff between condformat versions 0.2.0 dated 2016-03-07 and 0.4.0 dated 2016-07-25
DESCRIPTION | 26 - LICENSE | 1 MD5 | 59 +- NAMESPACE | 12 NEWS | 11 R/condformat.R | 5 R/condformat_render.R | 184 ++++++- R/rule_fill_discrete.R | 9 R/rule_fill_gradient.R | 2 R/rule_fill_gradient2.R | 3 R/show_columns.R | 21 R/show_rows.R | 2 README.md | 94 ++- build/vignette.rds |binary inst/doc/introduction.Rmd | 16 inst/doc/introduction.html | 789 +++++++++++++++++-------------- man/condformat.Rd | 5 man/condformat2excel.Rd |only man/condformat2latex.Rd |only man/knit_print.condformat_tbl.Rd |only man/render_rules_condformat_tbl.Rd | 4 man/rule_fill_discrete.Rd | 9 man/rule_fill_gradient.Rd | 2 man/rule_fill_gradient2.Rd | 3 man/show_columns.Rd | 21 man/show_rows.Rd | 2 tests/testthat/test_rendering.R | 34 - tests/testthat/test_rule_fill_discrete.R | 30 - tests/testthat/test_rule_fill_gradient.R | 11 tests/testthat/test_show.R | 43 - tests/testthat/test_theme_htmlTable.R | 4 vignettes/introduction.Rmd | 16 32 files changed, 889 insertions(+), 529 deletions(-)
Title: 0-1 Test for Chaos
Description: Computes and plot the results of the 0-1 test for chaos proposed
by Gottwald and Melbourne (2004) <DOI:10.1137/080718851>. The algorithm is
available in parallel for the independent values of parameter c.
Author: Tomas Martinovic [aut, cre]
Maintainer: Tomas Martinovic <tomas.martinovic@vsb.cz>
Diff between Chaos01 versions 1.0.0 dated 2016-07-18 and 1.0.1 dated 2016-07-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/Kc_computation.c | 16 ++++++++-------- 4 files changed, 17 insertions(+), 14 deletions(-)
Title: Coarse Approximation Linear Function
Description: Contains a greedy algorithm for coarse approximation linear
function.
Author: Stephanie Lane [aut, cre], Clark Jeffries [aut], Diana Perkins [aut]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between CALF versions 0.1.2 dated 2016-03-25 and 0.1.3 dated 2016-07-25
DESCRIPTION | 13 ++-- MD5 | 20 +++---- NAMESPACE | 1 R/CALF-package.R | 4 - R/calf_internal.R | 138 ++++++++++++++++++++++++++++++++++++++++---------- R/calf_wrappers.R | 89 +++++++++++++++++++++++--------- R/print.calf.R | 34 +++++++++--- man/CALF-package.Rd | 2 man/calf.Rd | 12 ++-- man/calf_randomize.Rd | 15 +++-- man/calf_subset.Rd | 15 +++-- 11 files changed, 254 insertions(+), 89 deletions(-)
Title: Modeling Framework for Cellular Communities in their
Environments
Description: Can be used for simulation of organisms living in
communities. Each organism is represented individually and genome scale
metabolic models determine the uptake and release of compounds. Biological
processes such as movement, diffusion, chemotaxis and kinetics are available
along with data analysis techniques.
Author: Eugen Bauer [aut],
Johannes Zimmermann [aut, cre]
Maintainer: Johannes Zimmermann <j.zimmermann@iem.uni-kiel.de>
Diff between BacArena versions 1.5.0 dated 2016-07-14 and 1.5.1 dated 2016-07-25
BacArena-1.5.0/BacArena/vignettes/BacArena-Introduction.html |only BacArena-1.5.1/BacArena/DESCRIPTION | 6 BacArena-1.5.1/BacArena/MD5 | 36 +- BacArena-1.5.1/BacArena/NEWS | 16 BacArena-1.5.1/BacArena/R/Arena.R | 2 BacArena-1.5.1/BacArena/R/Organism.R | 3 BacArena-1.5.1/BacArena/R/Stuff.R | 134 +++---- BacArena-1.5.1/BacArena/R/data.R |only BacArena-1.5.1/BacArena/data |only BacArena-1.5.1/BacArena/inst/doc/BacArena-Introduction.R | 100 ++++- BacArena-1.5.1/BacArena/inst/doc/BacArena-Introduction.Rmd | 190 ++++++++-- BacArena-1.5.1/BacArena/inst/doc/BacArena-Introduction.pdf |binary BacArena-1.5.1/BacArena/man/Organism-constructor.Rd | 2 BacArena-1.5.1/BacArena/man/colpal1.Rd |only BacArena-1.5.1/BacArena/man/colpal2.Rd |only BacArena-1.5.1/BacArena/man/colpal3.Rd |only BacArena-1.5.1/BacArena/man/colpal4.Rd |only BacArena-1.5.1/BacArena/man/colpal5.Rd |only BacArena-1.5.1/BacArena/man/colpal6.Rd |only BacArena-1.5.1/BacArena/man/openArena.Rd | 5 BacArena-1.5.1/BacArena/man/plotGrowthCurve.Rd | 4 BacArena-1.5.1/BacArena/man/sihumi_test.Rd |only BacArena-1.5.1/BacArena/vignettes/BacArena-Introduction.Rmd | 195 ++++++++--- 23 files changed, 474 insertions(+), 219 deletions(-)
Title: Bayesian Inference for the Multivariate Skew-t Model
Description: Estimates the multivariate skew-t and nested models, as described in the articles Liseo, B., Parisi, A. (2013). Bayesian inference for the multivariate skew-normal model: a population Monte Carlo approach. Comput. Statist. Data Anal. <doi:10.1016/j.csda.2013.02.007> and in Parisi, A., Liseo, B. Objective Bayesian analysis for the multivariate skew-t model (to appear).
Author: Antonio Parisi [aut, cre],
Brunero Liseo [aut],
Dirk Eddelbuettel [ctb],
Romain Francois [ctb]
Maintainer: Antonio Parisi <antonio.parisi@uniroma2.it>
Diff between mvst versions 1.0 dated 2016-07-20 and 1.0.1 dated 2016-07-25
mvst-1.0.1/mvst/DESCRIPTION | 17 +++++++++++++---- mvst-1.0.1/mvst/INSTALL | 6 ++++++ mvst-1.0.1/mvst/MD5 | 18 +++++++++--------- mvst-1.0.1/mvst/cleanup | 12 +++--------- mvst-1.0.1/mvst/configure | 24 ++++++++++-------------- mvst-1.0.1/mvst/configure.ac |only mvst-1.0.1/mvst/src/Makevars.in | 9 ++++----- mvst-1.0.1/mvst/src/Makevars.win | 11 ++++------- mvst-1.0.1/mvst/src/rvST.c | 12 ++++++------ mvst-1.0.1/mvst/src/rvT.c | 2 +- mvst-1.0/mvst/configure.in |only 11 files changed, 56 insertions(+), 55 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation.
Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 2.1-2 dated 2016-04-04 and 2.2-0 dated 2016-07-25
DESCRIPTION | 14 ++--- MD5 | 108 ++++++++++++++++++++--------------------- NAMESPACE | 2 R/jomo.MCMCchain.R | 2 R/jomo.R | 2 R/jomo1ran.MCMCchain.R | 16 +++--- R/jomo1ran.R | 16 +++--- R/jomo1rancat.MCMCchain.R | 4 - R/jomo1rancat.R | 4 - R/jomo1rancathr.MCMCchain.R | 6 +- R/jomo1rancathr.R | 6 +- R/jomo1rancon.MCMCchain.R | 4 - R/jomo1rancon.R | 4 - R/jomo1ranconhr.MCMCchain.R | 4 - R/jomo1ranconhr.R | 4 - R/jomo1ranmix.MCMCchain.R | 4 - R/jomo1ranmix.R | 4 - R/jomo1ranmixhr.MCMCchain.R | 6 +- R/jomo1ranmixhr.R | 6 +- R/jomo2.MCMCchain.R | 2 R/jomo2.R | 2 R/jomo2com.MCMCchain.R | 2 R/jomo2com.R | 2 R/jomo2hr.MCMCchain.R | 2 R/jomo2hr.R | 2 man/jomo.MCMCchain.Rd | 4 - man/jomo.Rd | 6 +- man/jomo1ran.MCMCchain.Rd | 4 - man/jomo1ran.Rd | 6 +- man/jomo1rancat.MCMCchain.Rd | 4 - man/jomo1rancat.Rd | 6 +- man/jomo1rancathr.MCMCchain.Rd | 4 - man/jomo1rancathr.Rd | 6 +- man/jomo1rancon.MCMCchain.Rd | 4 - man/jomo1rancon.Rd | 6 +- man/jomo1ranconhr.MCMCchain.Rd | 4 - man/jomo1ranconhr.Rd | 6 +- man/jomo1ranmix.MCMCchain.Rd | 4 - man/jomo1ranmix.Rd | 6 +- man/jomo1ranmixhr.MCMCchain.Rd | 4 - man/jomo1ranmixhr.Rd | 6 +- man/jomo2.MCMCchain.Rd | 4 - man/jomo2.Rd | 6 +- man/jomo2com.MCMCchain.Rd | 4 - man/jomo2com.Rd | 6 +- man/jomo2hr.MCMCchain.Rd | 4 - man/jomo2hr.Rd | 6 +- src/MCMCjomo1ranconhr.c | 37 ++++---------- src/MCMCjomo1ranmixhr.c | 40 +++++---------- src/MCMCjomo2hr.c | 40 +++++---------- src/jomo1ranconhr.c | 41 +++++---------- src/jomo1ranmixhr.c | 40 +++++---------- src/jomo2hr.c | 40 +++++---------- src/pdflib.c | 58 +++++++++++++++------- src/pdflib.h | 10 +-- 55 files changed, 300 insertions(+), 344 deletions(-)
Title: Perform JIVE Decompositions for Multi-Source Data
Description: Performs the JIVE decompositions on a list of data sets when the data share a dimension, returning low-rank matrices that capture the joint and individual structure of the data. It provides two methods of rank selection when the rank is unknown, a permutation test and a BIC selection algorithm. Also included in the package are three plotting functions for visualizing the variance attributed to each data source: a bar plot that shows the percentages of the variability attributable to joint and individual structure, a heatmap that shows the structure of the variability, and principal component plots.
Author: Michael J. O'Connell and Eric F. Lock
Maintainer: Michael J. O'Connell <oconn725@umn.edu>
Diff between r.jive versions 1.5 dated 2016-06-14 and 1.7 dated 2016-07-25
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- R/jive.r | 28 ++++++++++++++++------------ R/showHeatmaps.r | 24 +++++++++++++++--------- R/showPCA.r | 4 ++-- inst/doc/BRCA_Example.Rmd | 25 ++++++++++++------------- inst/doc/BRCA_Example.html | 26 +++++++++++++------------- man/jive.Rd | 7 +++++-- man/r.jive-package.Rd | 4 ++-- man/showHeatmaps.Rd | 2 +- man/showPCA.Rd | 6 +++++- vignettes/BRCA_Example.Rmd | 25 ++++++++++++------------- vignettes/HeatmapIndivMeth.png |binary vignettes/HeatmapsBRCA.png |binary vignettes/JointPCA.png |binary vignettes/MorePCA.png |binary vignettes/VarExplained.png |binary 17 files changed, 103 insertions(+), 88 deletions(-)
Title: Generalized Structured Component Analysis (GSCA)
Description: Fit a variety of component-based structural equation models.
Author: Heungsun Hwang, Sunmee Kim, Sungyoung Lee, Taesung Park
Maintainer: Sunmee Kim <sunmee.kim@mail.mcgill.ca>
Diff between gesca versions 1.0.2 dated 2016-05-04 and 1.0.3 dated 2016-07-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/gsca.mg.ho2.r | 17 +++++++++-------- R/gsca.mg.r | 17 +++++++++-------- 4 files changed, 25 insertions(+), 23 deletions(-)
Title: General Purpose Interface to 'Elasticsearch'
Description: Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java'
Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' 'API'
(<https://www.elastic.co/products/elasticsearch>), including functions for
setting connection details to 'Elasticsearch' instances, loading bulk data,
searching for documents with both 'HTTP' query variables and 'JSON' based body
requests. In addition, 'elastic' provides functions for interacting with 'APIs'
for 'indices', documents, nodes, clusters, an interface to the cat 'API', and
more.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between elastic versions 0.6.0 dated 2016-01-07 and 0.7.0 dated 2016-07-25
elastic-0.6.0/elastic/R/Search.R |only elastic-0.6.0/elastic/R/onstart.R |only elastic-0.7.0/elastic/DESCRIPTION | 18 elastic-0.7.0/elastic/MD5 | 82 ++-- elastic-0.7.0/elastic/NAMESPACE | 5 elastic-0.7.0/elastic/NEWS.md | 32 + elastic-0.7.0/elastic/R/Search_uri.R | 15 elastic-0.7.0/elastic/R/alias.R | 14 elastic-0.7.0/elastic/R/cat.r | 4 elastic-0.7.0/elastic/R/connect.R | 290 ++++++++++----- elastic-0.7.0/elastic/R/docs_bulk.r | 59 +-- elastic-0.7.0/elastic/R/docs_create.R | 8 elastic-0.7.0/elastic/R/docs_delete.R | 4 elastic-0.7.0/elastic/R/docs_get.r | 11 elastic-0.7.0/elastic/R/docs_mget.r | 8 elastic-0.7.0/elastic/R/elastic-package.r | 6 elastic-0.7.0/elastic/R/explain.R | 5 elastic-0.7.0/elastic/R/httr-verbs.R | 39 -- elastic-0.7.0/elastic/R/index.R | 31 - elastic-0.7.0/elastic/R/info.R |only elastic-0.7.0/elastic/R/mapping.R | 2 elastic-0.7.0/elastic/R/msearch.R | 4 elastic-0.7.0/elastic/R/mtermvectors.R |only elastic-0.7.0/elastic/R/nodes.R | 8 elastic-0.7.0/elastic/R/percolater.R | 11 elastic-0.7.0/elastic/R/scroll.R | 56 ++ elastic-0.7.0/elastic/R/search.r |only elastic-0.7.0/elastic/R/termvectors.R |only elastic-0.7.0/elastic/R/tokenizer_set.R | 4 elastic-0.7.0/elastic/R/zzz.r | 59 ++- elastic-0.7.0/elastic/README.md | 130 +++--- elastic-0.7.0/elastic/build/vignette.rds |binary elastic-0.7.0/elastic/inst/examples/omdb.json |only elastic-0.7.0/elastic/inst/ignore/connect_changes.R |only elastic-0.7.0/elastic/inst/ignore/omdb_data_fetch.R |only elastic-0.7.0/elastic/man/Search.Rd | 6 elastic-0.7.0/elastic/man/Search_uri.Rd | 4 elastic-0.7.0/elastic/man/connect.Rd | 55 ++ elastic-0.7.0/elastic/man/docs_bulk.Rd | 21 - elastic-0.7.0/elastic/man/es_auth.Rd | 11 elastic-0.7.0/elastic/man/info.Rd |only elastic-0.7.0/elastic/man/mtermvectors.Rd |only elastic-0.7.0/elastic/man/percolate.Rd | 3 elastic-0.7.0/elastic/man/scroll.Rd | 43 ++ elastic-0.7.0/elastic/man/termvectors.Rd |only elastic-0.7.0/elastic/tests/testthat/helper-elastic.R | 4 elastic-0.7.0/elastic/tests/testthat/test-count.R | 2 elastic-0.7.0/elastic/tests/testthat/test-mtermvectors.R |only elastic-0.7.0/elastic/tests/testthat/test-termvectors.R |only 49 files changed, 700 insertions(+), 354 deletions(-)