Title: Targeted Learning of a NP Importance of a Continuous Exposure
Description: Targeted minimum loss estimation (TMLE) of a non-parametric variable importance measure of a continuous exposure 'X' on an outcome 'Y', taking baseline covariates 'W' into account.
Author: Antoine Chambaz, Pierre Neuvial
Maintainer: Pierre Neuvial
Diff between tmle.npvi versions 0.8.1 dated 2014-02-08 and 0.9.3 dated 2015-02-05
tmle.npvi-0.8.1/tmle.npvi/man/SL.DSA.2.Rd |only tmle.npvi-0.8.1/tmle.npvi/man/SL.DSA.Rd |only tmle.npvi-0.8.1/tmle.npvi/man/predict.SL.DSA.Rd |only tmle.npvi-0.8.1/tmle.npvi/man/tmle.npvi.Rd |only tmle.npvi-0.9.3/tmle.npvi/DESCRIPTION | 18 tmle.npvi-0.9.3/tmle.npvi/MD5 | 77 ++- tmle.npvi-0.9.3/tmle.npvi/NAMESPACE | 34 + tmle.npvi-0.9.3/tmle.npvi/R/NPVI.R | 112 +++++ tmle.npvi-0.9.3/tmle.npvi/R/NPVI.update.R | 32 - tmle.npvi-0.9.3/tmle.npvi/R/NPVI.updatePsi.R | 6 tmle.npvi-0.9.3/tmle.npvi/R/SuperLearning.R |only tmle.npvi-0.9.3/tmle.npvi/R/estimateDevG.R | 3 tmle.npvi-0.9.3/tmle.npvi/R/estimateDevMu.R | 2 tmle.npvi-0.9.3/tmle.npvi/R/estimateDevTheta.R | 2 tmle.npvi-0.9.3/tmle.npvi/R/estimateG.R | 2 tmle.npvi-0.9.3/tmle.npvi/R/estimateMuAux.R | 2 tmle.npvi-0.9.3/tmle.npvi/R/estimateTheta.R | 2 tmle.npvi-0.9.3/tmle.npvi/R/getSample.R | 8 tmle.npvi-0.9.3/tmle.npvi/R/mu.R | 26 + tmle.npvi-0.9.3/tmle.npvi/R/pcor.R | 3 tmle.npvi-0.9.3/tmle.npvi/R/simulateData.R | 33 + tmle.npvi-0.9.3/tmle.npvi/R/simulateParsimoniouslyXgivenW.R | 214 ++++------- tmle.npvi-0.9.3/tmle.npvi/R/simulateParsimoniouslyYgivenXW.R | 122 ++---- tmle.npvi-0.9.3/tmle.npvi/R/theta.R | 131 ++++-- tmle.npvi-0.9.3/tmle.npvi/R/tmle.npvi.R | 103 ++++- tmle.npvi-0.9.3/tmle.npvi/R/validateArgumentObs.R | 2 tmle.npvi-0.9.3/tmle.npvi/build/vignette.rds |binary tmle.npvi-0.9.3/tmle.npvi/data/datalist |only tmle.npvi-0.9.3/tmle.npvi/data/learningLib.rda |binary tmle.npvi-0.9.3/tmle.npvi/data/superLearningLib.rda |binary tmle.npvi-0.9.3/tmle.npvi/data/tcga2012brca.rda |only tmle.npvi-0.9.3/tmle.npvi/inst/NEWS | 93 +--- tmle.npvi-0.9.3/tmle.npvi/inst/doc/tmle-npvi.R | 109 +++-- tmle.npvi-0.9.3/tmle.npvi/inst/doc/tmle-npvi.Rnw | 110 +++++ tmle.npvi-0.9.3/tmle.npvi/inst/doc/tmle-npvi.pdf |binary tmle.npvi-0.9.3/tmle.npvi/inst/testScripts |only tmle.npvi-0.9.3/tmle.npvi/man/getPValue.NPVI.Rd |only tmle.npvi-0.9.3/tmle.npvi/man/getPValue.matrix.Rd |only tmle.npvi-0.9.3/tmle.npvi/man/getSample.Rd | 8 tmle.npvi-0.9.3/tmle.npvi/man/tcga2012brca.Rd |only tmle.npvi-0.9.3/tmle.npvi/man/tmle.npvi..Rd |only tmle.npvi-0.9.3/tmle.npvi/vignettes/tmle-npvi.Rnw | 110 +++++ 42 files changed, 876 insertions(+), 488 deletions(-)
Title: Table Monster
Description: Provides a user friendly interface to generation of booktab style
tables using xtable.
Author: Grant Izmirlian Jr
Maintainer: Grant Izmirlian Jr
Diff between TableMonster versions 1.1 dated 2014-07-21 and 1.2 dated 2015-02-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/TableMonster.R | 31 ++++++++++++++++++++++++++++--- man/print.TableMonster.Rd | 8 +++++++- 4 files changed, 41 insertions(+), 10 deletions(-)
Title: Multivariate Normal Functions for Sparse Covariance and
Precision Matrices.
Description: Computes multivariate normal (MVN) densities, and
samples from MVN distributions, when the covariance or
precision matrix is sparse.
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun
Diff between sparseMVN versions 0.1.0 dated 2013-11-05 and 0.2.0 dated 2015-02-05
sparseMVN-0.1.0/sparseMVN/R/demo_funcs.R |only sparseMVN-0.1.0/sparseMVN/R/mvnSparse.R |only sparseMVN-0.1.0/sparseMVN/demo |only sparseMVN-0.1.0/sparseMVN/inst/doc/sparseMVN-vignette.Rnw |only sparseMVN-0.1.0/sparseMVN/inst/doc/sparseMVN-vignette.pdf |only sparseMVN-0.1.0/sparseMVN/inst/examples/tables.R |only sparseMVN-0.1.0/sparseMVN/man/rmvn-sparse.Rd |only sparseMVN-0.1.0/sparseMVN/vignettes/sparseMVN-vignette.Rnw |only sparseMVN-0.2.0/sparseMVN/DESCRIPTION | 26 + sparseMVN-0.2.0/sparseMVN/MD5 | 36 +- sparseMVN-0.2.0/sparseMVN/NAMESPACE | 7 sparseMVN-0.2.0/sparseMVN/NEWS | 18 + sparseMVN-0.2.0/sparseMVN/R/rmvn-sparse.R |only sparseMVN-0.2.0/sparseMVN/R/sparseMVN-package.R |only sparseMVN-0.2.0/sparseMVN/build/vignette.rds |binary sparseMVN-0.2.0/sparseMVN/inst/doc/sparseMVN-demo.R |only sparseMVN-0.2.0/sparseMVN/inst/doc/sparseMVN-demo.Rmd |only sparseMVN-0.2.0/sparseMVN/inst/doc/sparseMVN-demo.html |only sparseMVN-0.2.0/sparseMVN/inst/doc/timing.Rmd |only sparseMVN-0.2.0/sparseMVN/inst/doc/timing.pdf |only sparseMVN-0.2.0/sparseMVN/inst/examples/run_timing.Rmd |only sparseMVN-0.2.0/sparseMVN/inst/examples/timing.pdf |only sparseMVN-0.2.0/sparseMVN/man/rmvn.sparse.Rd |only sparseMVN-0.2.0/sparseMVN/man/sparseMVN-package.Rd | 33 +- sparseMVN-0.2.0/sparseMVN/tests |only sparseMVN-0.2.0/sparseMVN/vignettes/sparseMVN-demo.Rmd |only sparseMVN-0.2.0/sparseMVN/vignettes/sparseMVN.bib | 171 +++++++++---- sparseMVN-0.2.0/sparseMVN/vignettes/timing.Rmd |only sparseMVN-0.2.0/sparseMVN/vignettes/timing.html |only 29 files changed, 189 insertions(+), 102 deletions(-)
Title: R Interface to EPP-lab, a Java Program for Exploratory
Projection Pursuit
Description: An R Interface to EPP-lab v1.0. EPP-lab is a Java program for projection pursuit using genetic algorithms written by Alain Berro and S. Larabi Marie-Sainte and is included in the package.
Author: Daniel Fischer, Alain Berro, Klaus Nordhausen, Anne Ruiz-Gazen
Maintainer: Daniel Fischer
Diff between REPPlab versions 0.9 dated 2014-09-05 and 0.9.1 dated 2015-02-05
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- inst/ChangeLog | 4 ++++ man/REPPlab-package.Rd | 10 +++++----- 4 files changed, 20 insertions(+), 16 deletions(-)
Title: PANIC Tests of Nonstationarity
Description: This package contains a methodology that makes use of the factor
structure of large dimensional panels to understand the nature of
nonstationarity inherent in data. This is referred to as PANIC - Panel
Analysis of Nonstationarity in Idiosyncratic and Common Components. PANIC
(2004) includes valid pooling methods that allow panel unit root tests
tests to be constructed. PANIC (2004) can detect whether the
nonstationarity in a series is pervasive, or variable specific, or both.
PANIC (2010) includes the Panel Modified Sargan-Bhargava test, three models
for a Moon and Perron style test, and a bias correction for the
idiosyncratic unit root test of PANIC (2004). The PANIC model approximates
the number of factors based on Bai and Ng (2002).
Author: Steve Bronder
Maintainer: Steve Bronder
Diff between PANICr versions 0.0.0.2 dated 2014-10-24 and 0.0.0.5 dated 2015-02-05
PANICr-0.0.0.2/PANICr/inst/doc/PANICr.R |only PANICr-0.0.0.2/PANICr/vignettes/NIPAagg1.rda |only PANICr-0.0.0.2/PANICr/vignettes/NIPAagg2.rda |only PANICr-0.0.0.2/PANICr/vignettes/NIPAagg3.rda |only PANICr-0.0.0.5/PANICr/DESCRIPTION | 19 PANICr-0.0.0.5/PANICr/MD5 | 106 +-- PANICr-0.0.0.5/PANICr/R/MCMCfacstuffzzz.R | 306 ++++----- PANICr-0.0.0.5/PANICr/R/MCMCpanic10.R | 875 +++++++++++---------------- PANICr-0.0.0.5/PANICr/R/NIPAagg1.R | 26 PANICr-0.0.0.5/PANICr/R/NIPAagg2.R | 28 PANICr-0.0.0.5/PANICr/R/NIPAagg3.R | 26 PANICr-0.0.0.5/PANICr/R/adf04.r | 158 ++-- PANICr-0.0.0.5/PANICr/R/adf10.r | 166 ++--- PANICr-0.0.0.5/PANICr/R/adfc2.R | 22 PANICr-0.0.0.5/PANICr/R/adfnc.R | 22 PANICr-0.0.0.5/PANICr/R/adfp.r | 178 ++--- PANICr-0.0.0.5/PANICr/R/cPANIC.r | 412 ++++++------ PANICr-0.0.0.5/PANICr/R/coint0.R | 22 PANICr-0.0.0.5/PANICr/R/getnfac.r | 318 ++++----- PANICr-0.0.0.5/PANICr/R/glsd.r | 116 +-- PANICr-0.0.0.5/PANICr/R/lagn.R | 78 +- PANICr-0.0.0.5/PANICr/R/lm1.R | 22 PANICr-0.0.0.5/PANICr/R/minindc.r | 56 - PANICr-0.0.0.5/PANICr/R/mydiff.r | 66 +- PANICr-0.0.0.5/PANICr/R/myols.r | 30 PANICr-0.0.0.5/PANICr/R/nuisance.r | 114 +-- PANICr-0.0.0.5/PANICr/R/nw.r | 146 ++-- PANICr-0.0.0.5/PANICr/R/panic10b.r | 737 +++++++++++----------- PANICr-0.0.0.5/PANICr/R/pc.R | 80 +- PANICr-0.0.0.5/PANICr/R/pool10.r | 92 +- PANICr-0.0.0.5/PANICr/R/poolcoint.R | 94 +- PANICr-0.0.0.5/PANICr/R/s2ar.r | 174 ++--- PANICr-0.0.0.5/PANICr/R/trimr.r | 92 +- PANICr-0.0.0.5/PANICr/README.md | 18 PANICr-0.0.0.5/PANICr/build/vignette.rds |binary PANICr-0.0.0.5/PANICr/inst/doc/PANICr.Rmd | 127 --- PANICr-0.0.0.5/PANICr/inst/doc/PANICr.html | 497 +-------------- PANICr-0.0.0.5/PANICr/man/MCMCpanic04.Rd | 17 PANICr-0.0.0.5/PANICr/man/MCMCpanic10.Rd | 148 ++-- PANICr-0.0.0.5/PANICr/man/NIPAagg1.Rd | 26 PANICr-0.0.0.5/PANICr/man/NIPAagg2.Rd | 26 PANICr-0.0.0.5/PANICr/man/NIPAagg3.Rd | 26 PANICr-0.0.0.5/PANICr/man/adf.Rd | 50 - PANICr-0.0.0.5/PANICr/man/adfc2.Rd | 18 PANICr-0.0.0.5/PANICr/man/adfnc.Rd | 18 PANICr-0.0.0.5/PANICr/man/coint0.Rd | 18 PANICr-0.0.0.5/PANICr/man/getnfac.Rd | 94 +- PANICr-0.0.0.5/PANICr/man/lm1.Rd | 18 PANICr-0.0.0.5/PANICr/man/mydiff.Rd | 40 - PANICr-0.0.0.5/PANICr/man/nuisance.Rd | 50 - PANICr-0.0.0.5/PANICr/man/panic04.Rd | 85 +- PANICr-0.0.0.5/PANICr/man/panic10.Rd | 26 PANICr-0.0.0.5/PANICr/man/pool.Rd | 42 - PANICr-0.0.0.5/PANICr/man/s2ar.Rd | 72 +- PANICr-0.0.0.5/PANICr/man/trimr.Rd | 42 - PANICr-0.0.0.5/PANICr/vignettes/PANICr.Rmd | 127 --- 56 files changed, 2671 insertions(+), 3495 deletions(-)
Title: Symbolic Differentiation
Description: Compared to R functions deriv() and D(), Deriv() admits
user-defined function as well as function substitution
in arguments of functions to be differentiated.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol
Diff between Deriv versions 1.0 dated 2014-12-23 and 2.0 dated 2015-02-05
DESCRIPTION | 23 + MD5 | 24 + NAMESPACE | 2 NEWS | 33 ++ R/Deriv.R | 495 ++++++++++++++++---------------------- R/Simplify.R | 660 +++++++++++++++++++++++++++++++++++++++++++-------- README.md | 23 + inst |only man/Deriv-package.Rd | 60 +--- man/Deriv.Rd | 102 ++++--- man/Simplify.Rd |only man/format1.Rd |only tests |only 13 files changed, 932 insertions(+), 490 deletions(-)
Title: Default Bayesian Hypothesis Tests for Correlation, Partial
Correlation, and Mediation
Description: Default Bayesian hypothesis tests for correlation, partial correlation, and mediation
Author: Michele B. Nuijten, Ruud Wetzels, Dora Matzke, Conor V. Dolan, and Eric-Jan Wagenmakers
Maintainer: Michele B. Nuijten
Diff between BayesMed versions 1.0 dated 2014-01-28 and 1.0.1 dated 2015-02-05
BayesMed-1.0.1/BayesMed/DESCRIPTION | 12 ++++----- BayesMed-1.0.1/BayesMed/MD5 | 29 +++++++++++------------- BayesMed-1.0.1/BayesMed/R/print.jzs_med.R |only BayesMed-1.0.1/BayesMed/man/BayesMed-package.Rd | 25 ++++++++++++++------ BayesMed-1.0.1/BayesMed/man/Firefighters.Rd | 7 ++++- BayesMed-1.0.1/BayesMed/man/jzs_cor.Rd | 2 - BayesMed-1.0.1/BayesMed/man/jzs_corSD.Rd | 2 - BayesMed-1.0.1/BayesMed/man/jzs_med.Rd | 2 - BayesMed-1.0.1/BayesMed/man/jzs_medSD.Rd | 2 - BayesMed-1.0.1/BayesMed/man/jzs_partcor.Rd | 2 - BayesMed-1.0.1/BayesMed/man/jzs_partcorSD.Rd | 2 - BayesMed-1.0.1/BayesMed/man/plot.CI.Rd | 6 ++-- BayesMed-1.0.1/BayesMed/man/plot.JZSMed.Rd | 4 +-- BayesMed-1.0.1/BayesMed/man/plot.rjags.Rd | 10 ++++---- BayesMed-1.0.1/BayesMed/man/print.jzs_med.Rd |only BayesMed-1.0/BayesMed/R/print.JZSMedSD.R |only BayesMed-1.0/BayesMed/README.md |only BayesMed-1.0/BayesMed/man/print.JZSMed.Rd |only 18 files changed, 58 insertions(+), 47 deletions(-)
Title: SciViews GUI API - Functions to interface with Komodo Edit/IDE
Description: Functions to manage the GUI client, like Komodo with the
SciViews-K extension
Author: Philippe Grosjean [aut, cre]
Maintainer: Philippe Grosjean
Diff between svKomodo versions 0.9-62 dated 2014-03-02 and 0.9-63 dated 2015-02-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 6 ++++++ R/svKomodo-internal.R | 20 +++++++++++++++----- inst/NEWS.Rd | 8 +++++++- man/svKomodo-package.Rd | 4 ++-- 6 files changed, 39 insertions(+), 17 deletions(-)
Title: Meta-Analysis of Diagnostic Accuracy
Description: Provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutter&Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Holling et al. (2012) is also available. Standard methods like summary, plot and so on are provided.
Author: Philipp Doebler
Maintainer: Philipp Doebler
Diff between mada versions 0.5.6 dated 2014-07-23 and 0.5.7 dated 2015-02-05
DESCRIPTION | 17 +++----- MD5 | 30 +++++++-------- NAMESPACE | 8 ++++ R/reitsma.R | 56 ++++++++++++++++++++++++++++- R/rsSROC.R | 2 - build/vignette.rds |binary data/AuditC.rda |binary data/Dementia.rda |binary data/IAQ.rda |binary data/SAQ.rda |binary data/smoking.rda |binary inst/doc/mada.R | 97 +++++++++++++++++++++++++++++---------------------- inst/doc/mada.Rnw | 32 +++++++++++++--- inst/doc/mada.pdf |binary man/reitsma-class.Rd | 5 ++ vignettes/mada.Rnw | 32 +++++++++++++--- 16 files changed, 196 insertions(+), 83 deletions(-)
Title: Simulation of Longitudinal Data
Description: Simulation and visualization of complex
models for longitudinal data. The models are encoded using the model coding
language Mlxtran, automatically converted into C++ codes, compiled on the
fly and linked to R using the Rcpp package. That allows one to implement
very easily complex ODE-based models and complex statistical models,
including mixed effects models, for continuous, count, categorical, and
time-to-event data.
Author: Marc Lavielle [aut, cre],
Romain Francois [aut],
Fazia Bellal [ctb]
Maintainer: Marc Lavielle
Diff between mlxR versions 2.1.0 dated 2015-01-12 and 2.1.1 dated 2015-02-05
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/convertmlx.R | 10 ++++++++-- R/initMlxLibrary.R | 14 +++++++++----- 4 files changed, 24 insertions(+), 14 deletions(-)
Title: Interval Testing Procedure for Functional Data
Description: Implementation of the Interval Testing Procedure for functional data in different frameworks (i.e., one or two-population frameworks, functional linear models) by means of different basis expansions (i.e., B-spline, Fourier, and phase-amplitude Fourier). The current version of the package requires functional data evaluated on a uniform grid; it automatically projects each function on a chosen functional basis; it performs the entire family of multivariate tests; and, finally, it provides the matrix of the p-values of the previous tests and the vector of the corrected p-values. The functional basis, the coupled or uncoupled scenario, and the kind of test can be chosen by the user. The package provides also a plotting function creating a graphical output of the procedure: the p-value heat-map, the plot of the corrected p-values, and the plot of the functional data.
Author: Alessia Pini, Simone Vantini
Maintainer: Alessia Pini
Diff between fdatest versions 2.0 dated 2014-11-24 and 2.1 dated 2015-02-05
DESCRIPTION | 14 ++--- MD5 | 48 +++++++++--------- NAMESPACE | 8 +++ NEWS |only R/ITPaovbspline.R | 115 ++++++++++++++++++++++--------------------- R/ITPimage.R | 23 +++++--- R/ITPlmbspline.R | 124 +++++++++++++++-------------------------------- R/fdatest_2.1-internal.R |only R/plot.ITP1.R | 4 - R/plot.ITP2.R | 8 +-- data/NASAtemp.rda |binary man/ITP1bspline.Rd | 5 + man/ITP1fourier.Rd | 6 +- man/ITP2bspline.Rd | 14 ++--- man/ITP2fourier.Rd | 8 +-- man/ITP2pafourier.Rd | 7 +- man/ITPaovbspline.Rd | 7 +- man/ITPimage.Rd | 21 +------ man/ITPlmbspline.Rd | 8 +-- man/fdatest-package.Rd | 53 +++++++++++++++----- man/plot.ITP1.Rd | 11 ---- man/plot.ITP2.Rd | 10 --- man/plot.ITPaov.Rd | 8 +-- man/plot.ITPlm.Rd | 9 +-- man/summary.ITPaov.Rd | 13 ++-- man/summary.ITPlm.Rd | 13 ++-- 26 files changed, 259 insertions(+), 278 deletions(-)
Title: Survival Regression with Smoothed Error Distribution
Description: This package contains primarily a function to fit
a regression model with possibly right, left or interval
censored observations and with the error distribution
expressed as a mixture of G-splines. Core part
of the computation is done in compiled C++ written
using the Scythe Statistical Library Version 0.3.
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
Diff between smoothSurv versions 1.3-2 dated 2013-06-12 and 1.5 dated 2015-02-05
DESCRIPTION | 22 +++++++++--------- MD5 | 30 +++++++++++++----------- NAMESPACE | 9 ++++--- NEWS | 10 ++++++++ R/confint.smoothSurvReg.R |only R/estimTdiff.R | 50 ++++++++++++++++++++++++++++++----------- R/fdensity.smoothSurvReg.R | 4 +-- R/hazard.smoothSurvReg.R | 4 +-- R/print.estimTdiff.R | 29 +++++++++++++---------- R/smoothSurvReg.R | 45 +++++++++++++++++++++++------------- R/survfit.smoothSurvReg.R | 4 +-- inst/CITATION | 5 +--- man/confint.smoothSurvReg.Rd |only man/fdensity.smoothSurvReg.Rd | 6 +++- man/hazard.smoothSurvReg.Rd | 5 +++- man/residuals.smoothSurvReg.Rd | 2 - man/survfit.smoothSurvReg.Rd | 5 +++- 17 files changed, 145 insertions(+), 85 deletions(-)
Title: Estimation, Simulation and Visualization of Hierarchical
Archimedean Copulae (HAC)
Description: Package provides the estimation of the structure and the parameters, sampling methods and structural plots of Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin
Maintainer: Alexander Ristig
Diff between HAC versions 1.0-1 dated 2014-08-13 and 1.0-2 dated 2015-02-05
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++------- NAMESPACE | 4 +--- R/estimate.r | 36 +++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/ChangeLog | 8 ++++++++ inst/doc/HAC.pdf |binary man/estimate.copula.Rd | 2 +- 8 files changed, 56 insertions(+), 24 deletions(-)
Title: Bayesian Survival Regression with Flexible Error and Random
Effects Distributions
Description: Later
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
Diff between bayesSurv versions 2.3-1 dated 2014-08-09 and 2.4 dated 2015-02-05
CHANGES | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/CITATION | 5 ++--- 4 files changed, 13 insertions(+), 10 deletions(-)
Title: Phylogenetic Tools for comparative biology (and other things)
Description: phytools provides various functions for phylogenetic analysis,
mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
Diff between phytools versions 0.4-31 dated 2014-08-26 and 0.4-45 dated 2015-02-05
phytools-0.4-31/phytools/man/repPhylo.Rd |only phytools-0.4-45/phytools/DESCRIPTION | 10 phytools-0.4-45/phytools/MD5 | 294 +++++++++--------- phytools-0.4-45/phytools/NAMESPACE | 19 - phytools-0.4-45/phytools/R/densityMap.R | 17 - phytools-0.4-45/phytools/R/fancyTree.R | 9 phytools-0.4-45/phytools/R/fitPagel.R |only phytools-0.4-45/phytools/R/locate.fossil.R |only phytools-0.4-45/phytools/R/locate.yeti.R | 123 ++++++- phytools-0.4-45/phytools/R/pbtree.R | 7 phytools-0.4-45/phytools/R/phenogram.R | 15 phytools-0.4-45/phytools/R/plotSimmap.R | 138 +++++--- phytools-0.4-45/phytools/R/read.newick.R | 48 +- phytools-0.4-45/phytools/R/sim.history.R | 27 + phytools-0.4-45/phytools/R/utilities.R | 85 ++++- phytools-0.4-45/phytools/R/writeAncestors.R | 13 phytools-0.4-45/phytools/man/add.arrow.Rd |only phytools-0.4-45/phytools/man/add.color.bar.Rd | 3 phytools-0.4-45/phytools/man/add.everywhere.Rd | 3 phytools-0.4-45/phytools/man/add.random.Rd | 3 phytools-0.4-45/phytools/man/add.simmap.legend.Rd | 3 phytools-0.4-45/phytools/man/add.species.to.genus.Rd | 3 phytools-0.4-45/phytools/man/allFurcTrees.Rd | 2 phytools-0.4-45/phytools/man/anc.Bayes.Rd | 3 phytools-0.4-45/phytools/man/anc.ML.Rd | 5 phytools-0.4-45/phytools/man/anc.trend.Rd | 3 phytools-0.4-45/phytools/man/ancThresh.Rd | 4 phytools-0.4-45/phytools/man/applyBranchLengths.Rd | 3 phytools-0.4-45/phytools/man/ave.rates.Rd | 3 phytools-0.4-45/phytools/man/bind.tip.Rd | 3 phytools-0.4-45/phytools/man/bmPlot.Rd | 4 phytools-0.4-45/phytools/man/branching.diffusion.Rd | 3 phytools-0.4-45/phytools/man/brownie.lite.Rd | 2 phytools-0.4-45/phytools/man/brownieREML.Rd | 6 phytools-0.4-45/phytools/man/cladelabels.Rd | 4 phytools-0.4-45/phytools/man/collapse.to.star.Rd | 3 phytools-0.4-45/phytools/man/contMap.Rd | 6 phytools-0.4-45/phytools/man/countSimmap.Rd | 3 phytools-0.4-45/phytools/man/densityMap.Rd | 6 phytools-0.4-45/phytools/man/describe.simmap.Rd | 3 phytools-0.4-45/phytools/man/di2multi.simmap.Rd | 3 phytools-0.4-45/phytools/man/drop.clade.Rd | 3 phytools-0.4-45/phytools/man/drop.leaves.Rd | 3 phytools-0.4-45/phytools/man/drop.tip.contMap.Rd | 3 phytools-0.4-45/phytools/man/drop.tip.simmap.Rd | 3 phytools-0.4-45/phytools/man/estDiversity.Rd | 2 phytools-0.4-45/phytools/man/evol.rate.mcmc.Rd | 2 phytools-0.4-45/phytools/man/evol.vcv.Rd | 2 phytools-0.4-45/phytools/man/evolvcv.lite.Rd | 2 phytools-0.4-45/phytools/man/exhaustiveMP.Rd | 2 phytools-0.4-45/phytools/man/expm.Rd | 3 phytools-0.4-45/phytools/man/export.as.xml.Rd | 4 phytools-0.4-45/phytools/man/fancyTree.Rd | 3 phytools-0.4-45/phytools/man/fastAnc.Rd | 3 phytools-0.4-45/phytools/man/fastBM.Rd | 3 phytools-0.4-45/phytools/man/fastMRCA.Rd | 3 phytools-0.4-45/phytools/man/findMRCA.Rd | 3 phytools-0.4-45/phytools/man/fitBayes.Rd | 2 phytools-0.4-45/phytools/man/fitDiversityModel.Rd | 2 phytools-0.4-45/phytools/man/fitPagel.Rd |only phytools-0.4-45/phytools/man/gammatest.Rd | 2 phytools-0.4-45/phytools/man/genSeq.Rd | 3 phytools-0.4-45/phytools/man/getCladesofSize.Rd | 3 phytools-0.4-45/phytools/man/getDescendants.Rd | 3 phytools-0.4-45/phytools/man/getExtant.Rd | 3 phytools-0.4-45/phytools/man/getSisters.Rd | 3 phytools-0.4-45/phytools/man/getStates.Rd | 3 phytools-0.4-45/phytools/man/ladderize.simmap.Rd |only phytools-0.4-45/phytools/man/lambda.transform.Rd | 3 phytools-0.4-45/phytools/man/likMlambda.Rd | 3 phytools-0.4-45/phytools/man/locate.fossil.Rd |only phytools-0.4-45/phytools/man/locate.yeti.Rd | 8 phytools-0.4-45/phytools/man/ls.tree.Rd | 3 phytools-0.4-45/phytools/man/ltt.Rd | 2 phytools-0.4-45/phytools/man/ltt95.Rd | 3 phytools-0.4-45/phytools/man/make.era.map.Rd | 3 phytools-0.4-45/phytools/man/make.simmap.Rd | 6 phytools-0.4-45/phytools/man/map.overlap.Rd | 3 phytools-0.4-45/phytools/man/map.to.singleton.Rd | 3 phytools-0.4-45/phytools/man/matchNodes.Rd | 3 phytools-0.4-45/phytools/man/mergeMappedStates.Rd | 3 phytools-0.4-45/phytools/man/midpoint.root.Rd | 8 phytools-0.4-45/phytools/man/minRotate.Rd | 3 phytools-0.4-45/phytools/man/minSplit.Rd | 2 phytools-0.4-45/phytools/man/mrp.supertree.Rd | 10 phytools-0.4-45/phytools/man/multi.mantel.Rd | 2 phytools-0.4-45/phytools/man/multiC.Rd | 3 phytools-0.4-45/phytools/man/multiRF.Rd | 7 phytools-0.4-45/phytools/man/nodeHeights.Rd | 3 phytools-0.4-45/phytools/man/optim.phylo.ls.Rd | 4 phytools-0.4-45/phytools/man/orderMappedEdge.Rd | 3 phytools-0.4-45/phytools/man/paintSubTree.Rd | 3 phytools-0.4-45/phytools/man/paste.tree.Rd | 3 phytools-0.4-45/phytools/man/pbtree.Rd | 3 phytools-0.4-45/phytools/man/pgls.Ives.Rd | 4 phytools-0.4-45/phytools/man/phenogram.Rd | 11 phytools-0.4-45/phytools/man/phyl.RMA.Rd | 3 phytools-0.4-45/phytools/man/phyl.cca.Rd | 4 phytools-0.4-45/phytools/man/phyl.pairedttest.Rd | 4 phytools-0.4-45/phytools/man/phyl.pca.Rd | 4 phytools-0.4-45/phytools/man/phyl.resid.Rd | 6 phytools-0.4-45/phytools/man/phyl.vcv.Rd | 3 phytools-0.4-45/phytools/man/phylANOVA.Rd | 2 phytools-0.4-45/phytools/man/phylo.to.map.Rd | 3 phytools-0.4-45/phytools/man/phylo.toBackbone.Rd | 3 phytools-0.4-45/phytools/man/phyloDesign.Rd | 3 phytools-0.4-45/phytools/man/phylomorphospace.Rd | 6 phytools-0.4-45/phytools/man/phylomorphospace3d.Rd | 4 phytools-0.4-45/phytools/man/phylosig.Rd | 9 phytools-0.4-45/phytools/man/phytools-package.Rd | 2 phytools-0.4-45/phytools/man/plot.backbonePhylo.Rd | 3 phytools-0.4-45/phytools/man/plotBranchbyTrait.Rd | 3 phytools-0.4-45/phytools/man/plotSimmap.Rd | 6 phytools-0.4-45/phytools/man/plotThresh.Rd | 5 phytools-0.4-45/phytools/man/plotTree.Rd | 5 phytools-0.4-45/phytools/man/plotTree.wBars.Rd | 3 phytools-0.4-45/phytools/man/print.backbonePhylo.Rd | 3 phytools-0.4-45/phytools/man/ratebystate.Rd | 3 phytools-0.4-45/phytools/man/rateshift.Rd | 3 phytools-0.4-45/phytools/man/read.newick.Rd | 3 phytools-0.4-45/phytools/man/read.simmap.Rd | 6 phytools-0.4-45/phytools/man/reorder.backbonePhylo.Rd | 3 phytools-0.4-45/phytools/man/reorderSimmap.Rd | 3 phytools-0.4-45/phytools/man/rep.phylo.Rd |only phytools-0.4-45/phytools/man/reroot.Rd | 4 phytools-0.4-45/phytools/man/rerootingMethod.Rd | 7 phytools-0.4-45/phytools/man/rescaleSimmap.Rd | 3 phytools-0.4-45/phytools/man/rotateNodes.Rd | 3 phytools-0.4-45/phytools/man/roundBranches.Rd | 3 phytools-0.4-45/phytools/man/roundPhylogram.Rd | 3 phytools-0.4-45/phytools/man/rstate.Rd | 3 phytools-0.4-45/phytools/man/sampleFrom.Rd | 3 phytools-0.4-45/phytools/man/setMap.Rd | 5 phytools-0.4-45/phytools/man/sim.corrs.Rd | 5 phytools-0.4-45/phytools/man/sim.history.Rd | 8 phytools-0.4-45/phytools/man/sim.ratebystate.Rd | 3 phytools-0.4-45/phytools/man/sim.rates.Rd | 3 phytools-0.4-45/phytools/man/skewers.Rd | 2 phytools-0.4-45/phytools/man/splitTree.Rd | 3 phytools-0.4-45/phytools/man/splitplotTree.Rd | 3 phytools-0.4-45/phytools/man/starTree.Rd | 3 phytools-0.4-45/phytools/man/strahlerNumber.Rd | 3 phytools-0.4-45/phytools/man/threshBayes.Rd | 7 phytools-0.4-45/phytools/man/threshDIC.Rd | 5 phytools-0.4-45/phytools/man/threshState.Rd | 5 phytools-0.4-45/phytools/man/to.matrix.Rd | 3 phytools-0.4-45/phytools/man/treeSlice.Rd | 3 phytools-0.4-45/phytools/man/untangle.Rd | 3 phytools-0.4-45/phytools/man/vcvPhylo.Rd | 3 phytools-0.4-45/phytools/man/write.simmap.Rd | 4 phytools-0.4-45/phytools/man/writeAncestors.Rd | 3 phytools-0.4-45/phytools/man/writeNexus.Rd | 3 152 files changed, 941 insertions(+), 339 deletions(-)
Title: Knockoff Filter
Description: The knockoff filter is a procedure for controlling the false
discovery rate (FDR) when performing variable selection. For more information,
see the website below and the accompanying paper.
Author: Rina Foygel Barber, Emmanuel Candes, Evan Patterson
Maintainer: Evan Patterson
Diff between knockoff versions 0.1.1 dated 2014-12-20 and 0.2 dated 2015-02-05
DESCRIPTION | 13 ++++--- MD5 | 52 +++++++++++++++------------- NAMESPACE | 2 - NEWS |only R/create.R | 21 +++++------ R/knockoff.R | 12 ++++-- R/stats_lasso.R | 26 +++++++++----- R/util.R | 15 ++++++++ build/vignette.rds |binary inst/doc/intro.R | 5 ++ inst/doc/intro.Rmd | 10 +++++ inst/doc/intro.html | 10 ++++- inst/doc/sdp.Rmd | 14 +++++-- inst/doc/sdp.html | 13 ++++--- man/fs.Rd | 3 + man/knockoff.Rd | 3 + man/knockoff.create.Rd | 7 ++- man/knockoff.filter.Rd | 10 +++-- man/knockoff.stat.fs.Rd | 3 + man/knockoff.stat.lasso.Rd | 24 +++++++++--- man/knockoff.threshold.Rd | 3 + man/lasso_max_lambda.Rd | 3 + tests/testthat/InputStreamByteWrapper.class |only tests/testthat/MatlabServer.m |only tests/testthat/matlab_compat.R | 4 +- tests/testthat/test_create.R | 34 +++++++++++++++--- tests/testthat/test_util.R |only vignettes/intro.Rmd | 10 +++++ vignettes/sdp.Rmd | 14 +++++-- 29 files changed, 221 insertions(+), 90 deletions(-)
Title: Package to fit spatial data in gamlss
Description: Spatial models in gamlss
Author: Fernanda De Bastiani, Mikis Stasinopoulos,
Maintainer: Fernanda De Bastiani
Diff between gamlss.spatial versions 0.1 dated 2014-02-21 and 0.2 dated 2015-02-05
DESCRIPTION | 10 MD5 | 8 NAMESPACE | 11 - R/extraFunctions.R | 537 ++++++++++++++++++++++++++--------------------------- R/mrf-for-gamlss.R | 5 5 files changed, 287 insertions(+), 284 deletions(-)
More information about gamlss.spatial at CRAN
Permanent link
Title: Probabilistic Population Projection
Description: The package allows to generate population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova
Diff between bayesPop versions 5.2-1 dated 2014-11-20 and 5.2-2 dated 2015-02-05
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/get_outputs.R | 4 ++-- man/bayesPop-package.Rd | 7 ++++--- 5 files changed, 18 insertions(+), 13 deletions(-)