Title: Color Space Manipulation
Diff between colorspace versions 1.2-5 dated 2015-03-03 and 1.2-6 dated 2015-03-10
Description: Carries out mapping between assorted color spaces including
RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV),
CIELAB and polar CIELAB. Qualitative, sequential, and
diverging color palettes based on HCL colors are provided.
Author: Ross Ihaka [aut],
Paul Murrell [aut],
Kurt Hornik [aut],
Jason C. Fisher [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis
DESCRIPTION | 12 -
MD5 | 10 -
NAMESPACE | 1
NEWS | 6
R/choose_palette.R | 460 ++++++++++++++++++++++++------------------------
inst/doc/hcl-colors.pdf |binary
6 files changed, 247 insertions(+), 242 deletions(-)
Title: Rare Variants Association Analyses with Family Data
Diff between RVFam versions 1.0 dated 2015-02-19 and 1.1 dated 2015-03-10
Description: The RVFam package provides functions to perform single SNP association analyses and gene-based tests for continuous, binary and survival traits against sequencing data (e.g. exome chip) using family data.
Author: Ming-Huei Chen
Maintainer: Ming-Huei Chen
DESCRIPTION | 6 +++---
MD5 | 4 ++--
NAMESPACE | 6 ++++--
3 files changed, 9 insertions(+), 7 deletions(-)
Title: Mixture Models for Clustering and Classification
Diff between mixture versions 1.3 dated 2015-01-02 and 1.4 dated 2015-03-10
Description: An implementation of all 14 Gaussian parsimonious
clustering models (GPCMs) for model-based clustering and
model-based classification.
Author: Ryan P. Browne, Aisha ElSherbiny and Paul D. McNicholas
Maintainer: Ryan Browne
DESCRIPTION | 9 ++-
MD5 | 14 +++---
R/mixture.R | 68 ++++++++++++++++++++---------
man/gpcm.Rd | 2
man/mixture.Rd | 4 -
src/Makevars | 2
src/functions.h | 2
src/mixture.c | 129 +++++++++++++++++++++++++++++++++++++-------------------
8 files changed, 152 insertions(+), 78 deletions(-)
Title: Mixed Data Sampling Regression
Diff between midasr versions 0.3 dated 2014-04-30 and 0.4 dated 2015-03-10
Description: Methods and tools for mixed frequency time series data analysis. Allows estimation, model selection and forecasting for MIDAS regressions.
Author: Virmantas Kvedaras
Maintainer: Vaidotas Zemlys
midasr-0.3/midasr/man/AICc.Rd |only
midasr-0.3/midasr/man/almonp.gradient.Rd |only
midasr-0.3/midasr/man/checkARstar.Rd |only
midasr-0.3/midasr/man/gompertzp.gradient.Rd |only
midasr-0.3/midasr/man/hAh.test.Rd |only
midasr-0.3/midasr/man/hAhr.test.Rd |only
midasr-0.3/midasr/man/harstep.gradient.Rd |only
midasr-0.3/midasr/man/imidas_r.imidas_r.Rd |only
midasr-0.3/midasr/man/lcauchyp.gradient.Rd |only
midasr-0.3/midasr/man/midas.auto.sim.Rd |only
midasr-0.3/midasr/man/midas.sim.Rd |only
midasr-0.3/midasr/man/midas_coef.Rd |only
midasr-0.3/midasr/man/midas_r.midas_r.Rd |only
midasr-0.3/midasr/man/mls_coef.Rd |only
midasr-0.3/midasr/man/nakagamip.gradient.Rd |only
midasr-0.3/midasr/man/nbeta.gradient.Rd |only
midasr-0.3/midasr/man/nbetaMT.gradient.Rd |only
midasr-0.3/midasr/man/nealmon.gradient.Rd |only
midasr-0.3/midasr/man/polystep.gradient.Rd |only
midasr-0.3/midasr/man/prepmidas_r.Rd |only
midasr-0.3/midasr/man/simplearma.sim.Rd |only
midasr-0.3/midasr/man/weight_coef.Rd |only
midasr-0.3/midasr/man/weight_names.Rd |only
midasr-0.3/midasr/man/weight_param.Rd |only
midasr-0.4/midasr/DESCRIPTION | 10
midasr-0.4/midasr/LICENCE | 4
midasr-0.4/midasr/MD5 | 169 +++-----
midasr-0.4/midasr/NAMESPACE | 51 +-
midasr-0.4/midasr/NEWS | 22 +
midasr-0.4/midasr/R/imidasreg.R | 76 +--
midasr-0.4/midasr/R/lagspec.R | 28 -
midasr-0.4/midasr/R/midas_r_methods.R | 420 +++++++++++++-------
midasr-0.4/midasr/R/midasr-package.R | 9
midasr-0.4/midasr/R/midasreg.R | 512 +++++++++++++++----------
midasr-0.4/midasr/R/modsel.R | 150 +++----
midasr-0.4/midasr/R/nonparametric.R | 93 +++-
midasr-0.4/midasr/R/simulate.R | 252 ++++++++----
midasr-0.4/midasr/R/tests.R | 96 ++--
midasr-0.4/midasr/demo/RV.R | 26 -
midasr-0.4/midasr/demo/autoreg.R | 19
midasr-0.4/midasr/demo/imidasr.R | 17
midasr-0.4/midasr/demo/logRV.R | 28 -
midasr-0.4/midasr/demo/okun.R | 24 -
midasr-0.4/midasr/man/USpayems.Rd | 10
midasr-0.4/midasr/man/USqgdp.Rd | 10
midasr-0.4/midasr/man/USrealgdp.Rd | 8
midasr-0.4/midasr/man/USunempr.Rd | 8
midasr-0.4/midasr/man/agk.test.Rd | 12
midasr-0.4/midasr/man/almonp.Rd | 8
midasr-0.4/midasr/man/almonp_gradient.Rd |only
midasr-0.4/midasr/man/amidas_table.Rd | 75 +--
midasr-0.4/midasr/man/amweights.Rd | 26 -
midasr-0.4/midasr/man/average_forecast.Rd | 47 --
midasr-0.4/midasr/man/check_mixfreq.Rd | 15
midasr-0.4/midasr/man/coef.midas_r.Rd |only
midasr-0.4/midasr/man/deriv_tests.Rd | 15
midasr-0.4/midasr/man/deviance.midas_r.Rd | 6
midasr-0.4/midasr/man/dmls.Rd | 11
midasr-0.4/midasr/man/expand_amidas.Rd | 29 -
midasr-0.4/midasr/man/expand_weights_lags.Rd | 24 -
midasr-0.4/midasr/man/fmls.Rd | 16
midasr-0.4/midasr/man/forecast.midas_r.Rd | 66 ++-
midasr-0.4/midasr/man/get_estimation_sample.Rd | 4
midasr-0.4/midasr/man/gompertzp.Rd | 15
midasr-0.4/midasr/man/gompertzp_gradient.Rd |only
midasr-0.4/midasr/man/hAh_test.Rd |only
midasr-0.4/midasr/man/hAhr_test.Rd |only
midasr-0.4/midasr/man/harstep.Rd | 16
midasr-0.4/midasr/man/harstep_gradient.Rd |only
midasr-0.4/midasr/man/hf_lags_table.Rd | 58 --
midasr-0.4/midasr/man/imidas_r.Rd | 130 ++----
midasr-0.4/midasr/man/lcauchyp.Rd | 15
midasr-0.4/midasr/man/lcauchyp_gradient.Rd |only
midasr-0.4/midasr/man/lf_lags_table.Rd | 54 --
midasr-0.4/midasr/man/lws_table-add.Rd | 14
midasr-0.4/midasr/man/midas_auto_sim.Rd |only
midasr-0.4/midasr/man/midas_r.Rd | 151 +++----
midasr-0.4/midasr/man/midas_r.fit.Rd | 6
midasr-0.4/midasr/man/midas_r_ic_table.Rd | 56 --
midasr-0.4/midasr/man/midas_r_np.Rd | 21 -
midasr-0.4/midasr/man/midas_r_simple.Rd | 24 -
midasr-0.4/midasr/man/midas_sim.Rd |only
midasr-0.4/midasr/man/midas_u.Rd | 50 --
midasr-0.4/midasr/man/midasr-package.Rd | 14
midasr-0.4/midasr/man/mls.Rd | 15
midasr-0.4/midasr/man/modsel.Rd | 29 -
midasr-0.4/midasr/man/nakagamip.Rd | 15
midasr-0.4/midasr/man/nakagamip_gradient.Rd |only
midasr-0.4/midasr/man/nbeta.Rd | 14
midasr-0.4/midasr/man/nbetaMT.Rd | 16
midasr-0.4/midasr/man/nbetaMT_gradient.Rd |only
midasr-0.4/midasr/man/nbeta_gradient.Rd |only
midasr-0.4/midasr/man/nealmon.Rd | 18
midasr-0.4/midasr/man/nealmon_gradient.Rd |only
midasr-0.4/midasr/man/oos_prec.Rd | 9
midasr-0.4/midasr/man/plot_midas_coef.Rd |only
midasr-0.4/midasr/man/polystep.Rd | 11
midasr-0.4/midasr/man/polystep_gradient.Rd |only
midasr-0.4/midasr/man/predict.midas_r.Rd | 26 -
midasr-0.4/midasr/man/prep_hAh.Rd | 12
midasr-0.4/midasr/man/rvsp500.Rd | 9
midasr-0.4/midasr/man/select_and_forecast.Rd | 54 +-
midasr-0.4/midasr/man/simulate.midas_r.Rd |only
midasr-0.4/midasr/man/split_data.Rd | 22 -
midasr-0.4/midasr/man/update_weights.Rd |only
midasr-0.4/midasr/man/weights_table.Rd | 41 --
106 files changed, 1759 insertions(+), 1552 deletions(-)
Title: Kriging-Based Optimization for Computer Experiments
Diff between DiceOptim versions 1.4 dated 2013-04-04 and 1.5 dated 2015-03-10
Description: Expected Improvement. EGO algorithm. Multipoint EI and parallelized versions of EGO. Criteria and algorithms for Noisy Kriging-based Optimization , including AEI, AKG, EQI, and EI with plugin.
Author: D. Ginsbourger, V. Picheny, O. Roustant, with contributions by
C. Chevalier, S. Marmin, and T. Wagner
Maintainer: D. Ginsbourger
DiceOptim-1.4/DiceOptim/R/max_qEI.CL.R |only
DiceOptim-1.4/DiceOptim/man/CL.nsteps.Rd |only
DiceOptim-1.4/DiceOptim/man/max_qEI.CL.Rd |only
DiceOptim-1.5/DiceOptim/DESCRIPTION | 19
DiceOptim-1.5/DiceOptim/MD5 | 73 +--
DiceOptim-1.5/DiceOptim/NAMESPACE | 4
DiceOptim-1.5/DiceOptim/R/EI.R | 13
DiceOptim-1.5/DiceOptim/R/EI.grad.R | 13
DiceOptim-1.5/DiceOptim/R/max_EI.R | 4
DiceOptim-1.5/DiceOptim/R/max_qEI.R |only
DiceOptim-1.5/DiceOptim/R/qEGO.nsteps.R |only
DiceOptim-1.5/DiceOptim/R/qEI.R | 176 ++++++-
DiceOptim-1.5/DiceOptim/R/qEI.grad.R |only
DiceOptim-1.5/DiceOptim/R/sampleFromEI.R |only
DiceOptim-1.5/DiceOptim/man/AEI.Rd | 3
DiceOptim-1.5/DiceOptim/man/AEI.grad.Rd | 1
DiceOptim-1.5/DiceOptim/man/AKG.Rd | 1
DiceOptim-1.5/DiceOptim/man/AKG.grad.Rd | 4
DiceOptim-1.5/DiceOptim/man/DiceOptim-package.Rd | 33 -
DiceOptim-1.5/DiceOptim/man/EGO.nsteps.Rd | 446 +++++++++----------
DiceOptim-1.5/DiceOptim/man/EI.Rd | 10
DiceOptim-1.5/DiceOptim/man/EI.grad.Rd | 6
DiceOptim-1.5/DiceOptim/man/EQI.Rd | 1
DiceOptim-1.5/DiceOptim/man/EQI.grad.Rd | 7
DiceOptim-1.5/DiceOptim/man/branin2.Rd | 2
DiceOptim-1.5/DiceOptim/man/goldsteinprice.Rd | 1
DiceOptim-1.5/DiceOptim/man/hartman4.Rd | 2
DiceOptim-1.5/DiceOptim/man/kriging.quantile.Rd | 1
DiceOptim-1.5/DiceOptim/man/kriging.quantile.grad.Rd | 5
DiceOptim-1.5/DiceOptim/man/max_AEI.Rd | 4
DiceOptim-1.5/DiceOptim/man/max_AKG.Rd | 1
DiceOptim-1.5/DiceOptim/man/max_EI.Rd | 5
DiceOptim-1.5/DiceOptim/man/max_EQI.Rd | 4
DiceOptim-1.5/DiceOptim/man/max_qEI.Rd |only
DiceOptim-1.5/DiceOptim/man/min_quantile.Rd | 1
DiceOptim-1.5/DiceOptim/man/noisy.optimizer.Rd | 5
DiceOptim-1.5/DiceOptim/man/qEGO.nsteps.Rd |only
DiceOptim-1.5/DiceOptim/man/qEI.Rd | 164 +++---
DiceOptim-1.5/DiceOptim/man/qEI.grad.Rd |only
DiceOptim-1.5/DiceOptim/man/rosenbrock4.Rd | 2
DiceOptim-1.5/DiceOptim/man/sampleFromEI.Rd |only
DiceOptim-1.5/DiceOptim/man/sphere6.Rd | 2
DiceOptim-1.5/DiceOptim/man/update_km_noisyEGO.Rd | 4
43 files changed, 593 insertions(+), 424 deletions(-)
Title: Causal Inference Test
Diff between cit versions 1.3 dated 2014-12-10 and 1.4 dated 2015-03-10
Description: A formal statistical hypothesis test, resulting in a p-value, is provided to quantify uncertainty in a causal inference pertaining to a measured factor, e.g. a molecular species, which potentially mediates a known causal association between a locus and a quantitative trait. The test is applicable to data that includes genotype (discrete), possible causal mediator such as gene expression (continuous) and an outcome of interest (continuous).
Author: Joshua Millstein
Maintainer: Joshua Millstein
cit-1.3/cit/src/cit_v6.cpp |only
cit-1.4/cit/DESCRIPTION | 10 +++++-----
cit-1.4/cit/MD5 | 8 ++++----
cit-1.4/cit/man/cit-package.Rd | 2 +-
cit-1.4/cit/src/Makevars | 2 +-
cit-1.4/cit/src/cit_v7.cpp |only
6 files changed, 11 insertions(+), 11 deletions(-)
Title: Cut Numeric Values into Evenly Distributed Groups
Diff between binr versions 1.0 dated 2014-07-03 and 1.1 dated 2015-03-10
Description: Implementation of algorithms for cutting numerical values
exhibiting a potentially highly skewed distribution into evenly distributed
groups (bins). This functionality can be applied for binning discrete
values, such as counts, as well as for discretization of continuous values,
for example, during generation of features used in machine learning
algorithms.
Author: Sergei Izrailev
Maintainer: Sergei Izrailev
DESCRIPTION | 16 ++++++++--------
MD5 | 25 +++++++++++++------------
NAMESPACE | 2 +-
NEWS | 8 ++++++++
R/binr-package.R | 6 +++---
R/bins.R | 17 +++++++++++++----
README.md | 2 ++
inst/COPYRIGHTS | 1 +
inst/binr_1.1.pdf |only
man/binr.Rd | 9 +++++----
man/bins.Rd | 3 ++-
man/bins.greedy.Rd | 15 ++++++++-------
man/bins.optimize.Rd | 7 ++++---
man/bins.quantiles.Rd | 3 ++-
14 files changed, 70 insertions(+), 44 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Diff between qgraph versions 1.3 dated 2014-12-02 and 1.3.1 dated 2015-03-10
Description: The qgraph package can be used to visualize data as networks as well as provides an interface for visualizing weighted graphical models.
Author: Sacha Epskamp, Giulio Costantini, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp
qgraph-1.3.1/qgraph/DESCRIPTION | 15
qgraph-1.3.1/qgraph/MD5 | 48
qgraph-1.3.1/qgraph/NAMESPACE | 4
qgraph-1.3.1/qgraph/NEWS | 815 +++++-----
qgraph-1.3.1/qgraph/R/PLOT.R | 2376 +++++++++++++++----------------
qgraph-1.3.1/qgraph/R/addTitle.R | 2
qgraph-1.3.1/qgraph/R/averageLayout.R | 6
qgraph-1.3.1/qgraph/R/centrality.R | 2
qgraph-1.3.1/qgraph/R/centralityTable.R | 2
qgraph-1.3.1/qgraph/R/clusteringPlot.R | 3
qgraph-1.3.1/qgraph/R/clusteringTable.R | 2
qgraph-1.3.1/qgraph/R/cor_auto.R | 12
qgraph-1.3.1/qgraph/R/glasso_methods.R | 19
qgraph-1.3.1/qgraph/R/qgraph.R | 18
qgraph-1.3.1/qgraph/R/qgraph.panel.R | 118 -
qgraph-1.3.1/qgraph/R/qgraphAnnotate.R | 6
qgraph-1.3.1/qgraph/R/qgraph_loadings.R | 640 ++++----
qgraph-1.3.1/qgraph/R/qgraph_mixed.R |only
qgraph-1.3.1/qgraph/R/qgraph_svg.R | 358 ++--
qgraph-1.3.1/qgraph/R/scale2.R |only
qgraph-1.3.1/qgraph/README | 8
qgraph-1.3.1/qgraph/man/EBICglasso.Rd | 6
qgraph-1.3.1/qgraph/man/averageLayout.Rd | 5
qgraph-1.3.1/qgraph/man/cor_auto.Rd | 3
qgraph-1.3.1/qgraph/man/qgraph.Rd | 1
qgraph-1.3.1/qgraph/man/qgraphMixed.Rd |only
qgraph-1.3/qgraph/man/qgraph-package.Rd |only
27 files changed, 2266 insertions(+), 2203 deletions(-)
Title: Pretty Heatmaps
Diff between pheatmap versions 0.7.7 dated 2013-09-19 and 1.0.2 dated 2015-03-10
Description: A grid based implementation of heatmaps that offers more control
over heatmap dimensions and appearance.
Author: Raivo Kolde
Maintainer: Raivo Kolde
DESCRIPTION | 19
MD5 | 14
NAMESPACE | 4
NEWS | 38 +
R/pheatmap-package.r | 10
R/pheatmap.r | 1390 ++++++++++++++++++++++++++++--------------------
man/pheatmap-package.Rd | 10
man/pheatmap.Rd | 315 +++++-----
8 files changed, 1049 insertions(+), 751 deletions(-)
Title: Computation of Graphlet Orbit Counts in Sparse Graphs
Diff between orca versions 1.0 dated 2014-03-29 and 1.1 dated 2015-03-10
Description: Implements orbit counting using a fast combinatorial approach.
Counts orbits of nodes and edges from edge matrix or data frame, or a
graph object from the graph package.
Author: Tomaz Hocevar, Janez Demsar
Maintainer: Janez Demsar
DESCRIPTION | 16
MD5 | 24
R/orca.R | 26
data/petersen.txt.gz |only
data/usastates.txt.gz |only
data/yeast.txt.gz |only
man/karate.Rd | 2
man/orca.Rd | 31
man/petersen.Rd |only
man/usastates.Rd |only
man/yeast.Rd |only
src/count.cpp | 410 +++++------
tests/karate-as-matrix.Rout.save | 113 +--
tests/karate.Rout.save | 1411 +++++++++++++++------------------------
tests/permutation.R |only
tests/permutation.Rout.save |only
tests/symmetry.R |only
tests/symmetry.Rout.save |only
18 files changed, 892 insertions(+), 1141 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Diff between ChemoSpec versions 3.0-1 dated 2015-01-21 and 4.0-0 dated 2015-03-10
Description: A collection of functions for plotting spectra (NMR, IR, Raman) and carrying out various forms of top-down exploratory data analysis, such as HCA, PCA, model-based clustering and STOCSY analysis. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette illustrating typical operations is available.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson
ChemoSpec-3.0-1/ChemoSpec/R/LoopThruSpectra.R |only
ChemoSpec-3.0-1/ChemoSpec/R/aovPCA.R |only
ChemoSpec-3.0-1/ChemoSpec/R/baselineSpec.R |only
ChemoSpec-3.0-1/ChemoSpec/R/binBuck.R |only
ChemoSpec-3.0-1/ChemoSpec/R/calcSN.R |only
ChemoSpec-3.0-1/ChemoSpec/R/classPCA.R |only
ChemoSpec-3.0-1/ChemoSpec/R/findTMS.R |only
ChemoSpec-3.0-1/ChemoSpec/R/pcaBoot.R |only
ChemoSpec-3.0-1/ChemoSpec/R/readBrukerAscii.R |only
ChemoSpec-3.0-1/ChemoSpec/R/readBrukerTxt.R |only
ChemoSpec-3.0-1/ChemoSpec/R/robPCA.R |only
ChemoSpec-3.0-1/ChemoSpec/R/specSurvey.R |only
ChemoSpec-3.0-1/ChemoSpec/data/CuticleIR.RData |only
ChemoSpec-3.0-1/ChemoSpec/man/CuticleIR.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/LoopThruSpectra.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/aovPCA.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/baselineSpec.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/binBuck.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/calcSN.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/classPCA.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/findTMS.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/pcaBoot.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/readBrukerTxt.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/robPCA.Rd |only
ChemoSpec-3.0-1/ChemoSpec/man/specSurvey.Rd |only
ChemoSpec-4.0-0/ChemoSpec/DESCRIPTION | 19
ChemoSpec-4.0-0/ChemoSpec/MD5 | 210 ++---
ChemoSpec-4.0-0/ChemoSpec/NAMESPACE | 136 ++-
ChemoSpec-4.0-0/ChemoSpec/NEWS | 639 +++++++---------
ChemoSpec-4.0-0/ChemoSpec/R/aovPCAloadings.R | 4
ChemoSpec-4.0-0/ChemoSpec/R/aovPCAscores.R | 8
ChemoSpec-4.0-0/ChemoSpec/R/aov_pcaSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/avgFacLvls.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/baselineSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/binSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/c_pcaSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/chooseLvls.R |only
ChemoSpec-4.0-0/ChemoSpec/R/clupaSpectra.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/corSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/covSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/cv_pcaSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/evalClusters.R | 20
ChemoSpec-4.0-0/ChemoSpec/R/files2SpectraObject.R | 238 ++---
ChemoSpec-4.0-0/ChemoSpec/R/getMaxCovByFreq.R |only
ChemoSpec-4.0-0/ChemoSpec/R/hcaSpectra.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/hmapSpectra.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/loopThruSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/mclust3D.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/mclust3dSpectra.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/mclustSpectra.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/plotSpectraJS.R |only
ChemoSpec-4.0-0/ChemoSpec/R/r_pcaSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/rowDist.R | 25
ChemoSpec-4.0-0/ChemoSpec/R/sampleDistSpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/R/splitSpectraGroups.R | 2
ChemoSpec-4.0-0/ChemoSpec/R/surveySpectra.R |only
ChemoSpec-4.0-0/ChemoSpec/build/vignette.rds |binary
ChemoSpec-4.0-0/ChemoSpec/data/alignMUD.RData |only
ChemoSpec-4.0-0/ChemoSpec/data/datalist | 4
ChemoSpec-4.0-0/ChemoSpec/data/metMUD1.RData |only
ChemoSpec-4.0-0/ChemoSpec/data/metMUD2.RData |only
ChemoSpec-4.0-0/ChemoSpec/inst/doc/ChemoSpec.R | 19
ChemoSpec-4.0-0/ChemoSpec/inst/doc/ChemoSpec.Rnw | 61 -
ChemoSpec-4.0-0/ChemoSpec/inst/doc/ChemoSpec.pdf |binary
ChemoSpec-4.0-0/ChemoSpec/inst/extdata |only
ChemoSpec-4.0-0/ChemoSpec/man/ChemoSpec-package.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/MUD.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/Spectra.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/SrE.IR.Rd | 13
ChemoSpec-4.0-0/ChemoSpec/man/aovPCAloadings.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/aovPCAscores.Rd | 14
ChemoSpec-4.0-0/ChemoSpec/man/aov_pcaSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/avgFacLvls.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/baselineSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/binData.Rd | 4
ChemoSpec-4.0-0/ChemoSpec/man/binSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/c_pcaSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/check4Gaps.Rd | 9
ChemoSpec-4.0-0/ChemoSpec/man/chkSpectra.Rd | 20
ChemoSpec-4.0-0/ChemoSpec/man/chooseLvls.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/clupaSpectra.Rd | 26
ChemoSpec-4.0-0/ChemoSpec/man/colLeaf.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/colorSymbol.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/conColScheme.Rd | 14
ChemoSpec-4.0-0/ChemoSpec/man/coordProjCS.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/corSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/cv_pcaSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/evalClusters.Rd | 56 -
ChemoSpec-4.0-0/ChemoSpec/man/files2SpectraObject.Rd | 24
ChemoSpec-4.0-0/ChemoSpec/man/getMaxCovByFreq.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/groupNcolor.Rd | 7
ChemoSpec-4.0-0/ChemoSpec/man/hcaScores.Rd | 10
ChemoSpec-4.0-0/ChemoSpec/man/hcaSpectra.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/hmapSpectra.Rd | 4
ChemoSpec-4.0-0/ChemoSpec/man/hypTestScores.Rd | 22
ChemoSpec-4.0-0/ChemoSpec/man/isWholeNo.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/labelExtremes.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/labelExtremes3d.Rd | 4
ChemoSpec-4.0-0/ChemoSpec/man/loopThruSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/makeEllipsoid.Rd | 5
ChemoSpec-4.0-0/ChemoSpec/man/mclust3D.Rd | 4
ChemoSpec-4.0-0/ChemoSpec/man/mclust3dSpectra.Rd | 10
ChemoSpec-4.0-0/ChemoSpec/man/mclustSpectra.Rd | 14
ChemoSpec-4.0-0/ChemoSpec/man/normSpectra.Rd | 13
ChemoSpec-4.0-0/ChemoSpec/man/normVec.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/pcaDiag.Rd | 9
ChemoSpec-4.0-0/ChemoSpec/man/plot2Loadings.Rd | 8
ChemoSpec-4.0-0/ChemoSpec/man/plotHCA.Rd | 4
ChemoSpec-4.0-0/ChemoSpec/man/plotLoadings.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/plotScores.Rd | 19
ChemoSpec-4.0-0/ChemoSpec/man/plotScores3D.Rd | 12
ChemoSpec-4.0-0/ChemoSpec/man/plotScoresCor.Rd | 2
ChemoSpec-4.0-0/ChemoSpec/man/plotScoresDecoration.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/plotScoresRGL.Rd | 10
ChemoSpec-4.0-0/ChemoSpec/man/plotScree.Rd | 17
ChemoSpec-4.0-0/ChemoSpec/man/plotSpectra.Rd | 18
ChemoSpec-4.0-0/ChemoSpec/man/plotSpectraJS.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/q2rPCA.Rd | 3
ChemoSpec-4.0-0/ChemoSpec/man/r_pcaSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/readJDX.Rd | 5
ChemoSpec-4.0-0/ChemoSpec/man/removeFreq.Rd | 20
ChemoSpec-4.0-0/ChemoSpec/man/removeSample.Rd | 18
ChemoSpec-4.0-0/ChemoSpec/man/rowDist.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/sPlotSpectra.Rd | 7
ChemoSpec-4.0-0/ChemoSpec/man/sampleDistSpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/man/shrinkLeaf.Rd | 6
ChemoSpec-4.0-0/ChemoSpec/man/splitSpectraGroups.Rd | 38
ChemoSpec-4.0-0/ChemoSpec/man/sumGroups.Rd | 8
ChemoSpec-4.0-0/ChemoSpec/man/sumSpectra.Rd | 10
ChemoSpec-4.0-0/ChemoSpec/man/surveySpectra.Rd |only
ChemoSpec-4.0-0/ChemoSpec/vignettes/ChemoSpec.Rnw | 61 -
ChemoSpec-4.0-0/ChemoSpec/vignettes/MetabPreProcess.pdf |only
132 files changed, 1025 insertions(+), 982 deletions(-)
Title: Code Analysis Tools for R
Diff between codetools versions 0.2-10 dated 2015-01-17 and 0.2-11 dated 2015-03-10
Description: Code analysis tools for R.
Author: Luke Tierney
Maintainer: Luke Tierney
DESCRIPTION | 8 ++++----
MD5 | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
Title: Advanced Forest Plot Using 'grid' Graphics
Diff between forestplot versions 1.0 dated 2014-12-29 and 1.1 dated 2015-03-10
Description: The plot allows for multiple confidence intervals per row,
custom fonts for each text element,
custom confidence intervals,
text mixed with expressions, and more.
The aim is to extend the use of forest plots beyond meta-analyses.
This is a more general version of the original 'rmeta' package's forestplot
function and relies heavily on the 'grid' package.
Author: Max Gordon [aut, cre],
Thomas Lumley [aut, ctb]
Maintainer: Max Gordon
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-10-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-2-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-3-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-4-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-5-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-6-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-7-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-8-1.svg |only
forestplot-1.0/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-9-1.svg |only
forestplot-1.1/forestplot/DESCRIPTION | 8
forestplot-1.1/forestplot/MD5 | 59 +-
forestplot-1.1/forestplot/NEWS | 10
forestplot-1.1/forestplot/R/forestplot-package.R | 22
forestplot-1.1/forestplot/R/forestplot.R | 138 ++++--
forestplot-1.1/forestplot/R/forestplot_helpers.R | 56 +-
forestplot-1.1/forestplot/R/private.R | 227 +++++++++-
forestplot-1.1/forestplot/inst/doc/forestplot.R | 58 +-
forestplot-1.1/forestplot/inst/doc/forestplot.Rmd | 92 +++-
forestplot-1.1/forestplot/inst/doc/forestplot.html | 103 +++-
forestplot-1.1/forestplot/man/forestplot-package.Rd | 21
forestplot-1.1/forestplot/man/forestplot.Rd | 58 ++
forestplot-1.1/forestplot/man/fpColors.Rd | 5
forestplot-1.1/forestplot/man/prFpDrawLines.Rd |only
forestplot-1.1/forestplot/man/prFpGetGraphTicksAndClips.Rd | 9
forestplot-1.1/forestplot/man/prFpGetLabels.Rd | 6
forestplot-1.1/forestplot/man/prFpGetLines.Rd |only
forestplot-1.1/forestplot/man/prFpPrintLabels.Rd | 7
forestplot-1.1/forestplot/man/prGparMerge.Rd |only
forestplot-1.1/forestplot/tests/testthat/test-prFpGetLines.R |only
forestplot-1.1/forestplot/tests/testthat/test-prGparMerge.R |only
forestplot-1.1/forestplot/vignettes/forestplot.Rmd | 92 +++-
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/Thumbs.db |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-10-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-11-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-12-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-13-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-2-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-3-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-4-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-5-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-6-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-7-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-8-1.png |only
forestplot-1.1/forestplot/vignettes/forestplot_files/figure-html/unnamed-chunk-9-1.png |only
44 files changed, 748 insertions(+), 223 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Diff between eVenn versions 2.1.6 dated 2012-07-12 and 2.2 dated 2015-03-10
Description: Compute a matrix comparison of lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard
eVenn-2.1.6/eVenn/R/evenn.r |only
eVenn-2.1.6/eVenn/data/res2.rda |only
eVenn-2.1.6/eVenn/data/res3.rda |only
eVenn-2.1.6/eVenn/data/res4.rda |only
eVenn-2.1.6/eVenn/man/res2.Rd |only
eVenn-2.1.6/eVenn/man/res3.Rd |only
eVenn-2.1.6/eVenn/man/res4.Rd |only
eVenn-2.2/eVenn/DESCRIPTION | 23 +-
eVenn-2.2/eVenn/MD5 | 30 ++-
eVenn-2.2/eVenn/NAMESPACE | 6
eVenn-2.2/eVenn/R/autoevenn.R |only
eVenn-2.2/eVenn/R/evenn.R |only
eVenn-2.2/eVenn/R/man.evenn.R | 106 +++++++------
eVenn-2.2/eVenn/data/Data_Binary_Matrix.rda |only
eVenn-2.2/eVenn/data/Data_Lists.rda |only
eVenn-2.2/eVenn/data/Data_Matrix_Of_Folds.rda |only
eVenn-2.2/eVenn/data/Data_Matrix_Of_Ratios.rda |only
eVenn-2.2/eVenn/man/Data_Binary_Matrix.Rd |only
eVenn-2.2/eVenn/man/Data_Lists.Rd |only
eVenn-2.2/eVenn/man/Data_Matrix_Of_Folds.Rd |only
eVenn-2.2/eVenn/man/Data_Matrix_Of_Ratios.Rd |only
eVenn-2.2/eVenn/man/autoevenn.Rd |only
eVenn-2.2/eVenn/man/eVenn-package.Rd | 110 +++++++-------
eVenn-2.2/eVenn/man/evenn.Rd | 192 ++++++++++++++-----------
eVenn-2.2/eVenn/man/man.evenn.Rd | 36 ++--
25 files changed, 278 insertions(+), 225 deletions(-)
Title: Bayesian Additive Regression Trees
Diff between bartMachine versions 1.1.1 dated 2014-12-02 and 1.2.0 dated 2015-03-10
Description: An advanced implementation of Bayesian Additive Regression Trees with expanded features for data analysis and visualization.
Author: Adam Kapelner and Justin Bleich (R package), see COPYRIGHTS file for the authors of the java libraries
Maintainer: Adam Kapelner
CHANGELOG | 14 ++++
DESCRIPTION | 10 +--
MD5 | 32 +++++------
R/bartMachine.R | 30 +++-------
R/bart_package_builders.R | 13 +++-
R/bart_package_inits.R | 6 +-
R/bart_package_plots.R | 23 ++++---
R/zzz.R | 3 -
inst/doc/bartMachine.pdf |binary
inst/java/bart_java.jar |binary
java/bartMachine/bartMachineClassification.java | 4 +
java/bartMachine/bartMachineRegression.java | 1
java/bartMachine/bartMachineRegressionMultThread.java | 8 ++
java/bartMachine/bartMachineTreeNode.java | 52 +++++++++---------
java/bartMachine/bartMachine_a_base.java | 2
java/bartMachine/bartMachine_g_mh.java | 7 --
man/bartMachine.Rd | 9 ++-
17 files changed, 120 insertions(+), 94 deletions(-)
Title: Relational Event Models
Diff between relevent versions 1.0-3 dated 2013-04-03 and 1.0-4 dated 2015-03-10
Description: Tools to fit relational event models.
Author: Carter T. Butts
Maintainer: Carter T. Butts
ChangeLog | 7 +++++++
DESCRIPTION | 11 +++++------
MD5 | 11 ++++++-----
NAMESPACE | 3 +++
R/rem.R | 11 +++++------
R/rem.dyad.R | 4 +---
inst |only
7 files changed, 27 insertions(+), 20 deletions(-)
Title: Parallel Programming Tools for Rcpp
Diff between RcppParallel versions 4.3.4 dated 2015-03-07 and 4.3.6 dated 2015-03-10
Description: High level functions for doing parallel programming with Rcpp.
For example, the parallelFor function can be used to convert the work of
a standard serial "for" loop into a parallel one and the parallelReduce
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut, cre],
Romain Francois [aut, cph],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/),
RStudio [cph],
Intel [aut, cph] (Intel TBB library,
https://www.threadingbuildingblocks.org/),
Microsoft [cph]
Maintainer: JJ Allaire
DESCRIPTION | 10 +++++-----
MD5 | 22 +++++++++++-----------
NEWS | 7 +++++++
R/build.R | 9 +++++++--
inst/include/tbb/concurrent_vector.h | 4 ++--
src/Makevars | 11 ++++++-----
src/options.cpp | 4 ++++
src/tbb/build/windows.inc | 18 ++++++++++++------
src/tbb/include/tbb/concurrent_vector.h | 4 ++--
tests/testthat/cpp/distance.cpp | 2 +-
tests/testthat/cpp/transform.cpp | 23 +++++++++++++----------
tests/testthat/test-transform.R | 2 +-
12 files changed, 71 insertions(+), 45 deletions(-)
Title: R Wrapper for the Energy Information Administration (EIA) API
Diff between EIAdata versions 0.0.2 dated 2014-12-16 and 0.0.3 dated 2015-03-10
Description: An R wrapper to allow the user to query categories and Series IDs, and import data, from the EIA's API.
Author: Matthew Brigida
Maintainer: Matthew Brigida
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
man/EIAdata-package.Rd | 9 ++++++---
man/getCatEIA.Rd | 44 +++++++++++++++++++++++++++++---------------
4 files changed, 42 insertions(+), 25 deletions(-)
Title: Graph Estimation Based on Birth-Death MCMC Approach
Diff between BDgraph versions 2.16 dated 2015-02-27 and 2.17 dated 2015-03-10
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
BDgraph-2.16/BDgraph/R/I.g.R |only
BDgraph-2.16/BDgraph/man/I.g.Rd |only
BDgraph-2.17/BDgraph/DESCRIPTION | 6 +++---
BDgraph-2.17/BDgraph/MD5 | 24 ++++++++++++++----------
BDgraph-2.17/BDgraph/NAMESPACE | 1 -
BDgraph-2.17/BDgraph/R/bdgraph.R | 14 ++++++++++----
BDgraph-2.17/BDgraph/R/phat.R | 15 ++++++++-------
BDgraph-2.17/BDgraph/R/plotcoda.R | 22 +++++++++++++++-------
BDgraph-2.17/BDgraph/R/select.R | 16 ++++++++--------
BDgraph-2.17/BDgraph/build |only
BDgraph-2.17/BDgraph/inst |only
BDgraph-2.17/BDgraph/man/plotcoda.Rd | 4 +++-
BDgraph-2.17/BDgraph/src/BDgraph.cpp | 19 +++++++++++++++++++
BDgraph-2.17/BDgraph/vignettes |only
14 files changed, 80 insertions(+), 41 deletions(-)