Title: Targeted Learning of a NP Importance of a Continuous Exposure
Diff between tmle.npvi versions 0.8.1 dated 2014-02-08 and 0.9.3 dated 2015-02-05
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
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
Diff between TableMonster versions 1.1 dated 2014-07-21 and 1.2 dated 2015-02-05
Description: Provides a user friendly interface to generation of booktab style
tables using xtable.
Author: Grant Izmirlian Jr
Maintainer: Grant Izmirlian Jr
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.
Diff between sparseMVN versions 0.1.0 dated 2013-11-05 and 0.2.0 dated 2015-02-05
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
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
Diff between REPPlab versions 0.9 dated 2014-09-05 and 0.9.1 dated 2015-02-05
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
DESCRIPTION | 16 ++++++++--------
MD5 | 6 +++---
inst/ChangeLog | 4 ++++
man/REPPlab-package.Rd | 10 +++++-----
4 files changed, 20 insertions(+), 16 deletions(-)
Title: PANIC Tests of Nonstationarity
Diff between PANICr versions 0.0.0.2 dated 2014-10-24 and 0.0.0.5 dated 2015-02-05
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
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
Diff between Deriv versions 1.0 dated 2014-12-23 and 2.0 dated 2015-02-05
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
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
Diff between BayesMed versions 1.0 dated 2014-01-28 and 1.0.1 dated 2015-02-05
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
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
Diff between svKomodo versions 0.9-62 dated 2014-03-02 and 0.9-63 dated 2015-02-05
Description: Functions to manage the GUI client, like Komodo with the
SciViews-K extension
Author: Philippe Grosjean [aut, cre]
Maintainer: Philippe Grosjean
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
Diff between mada versions 0.5.6 dated 2014-07-23 and 0.5.7 dated 2015-02-05
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
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
Diff between mlxR versions 2.1.0 dated 2015-01-12 and 2.1.1 dated 2015-02-05
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
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
Diff between fdatest versions 2.0 dated 2014-11-24 and 2.1 dated 2015-02-05
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
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
Diff between smoothSurv versions 1.3-2 dated 2013-06-12 and 1.5 dated 2015-02-05
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
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)
Diff between HAC versions 1.0-1 dated 2014-08-13 and 1.0-2 dated 2015-02-05
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
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
Diff between bayesSurv versions 2.3-1 dated 2014-08-09 and 2.4 dated 2015-02-05
Description: Later
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
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)
Diff between phytools versions 0.4-31 dated 2014-08-26 and 0.4-45 dated 2015-02-05
Description: phytools provides various functions for phylogenetic analysis,
mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
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
Diff between knockoff versions 0.1.1 dated 2014-12-20 and 0.2 dated 2015-02-05
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
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
Diff between gamlss.spatial versions 0.1 dated 2014-02-21 and 0.2 dated 2015-02-05
More information about gamlss.spatial at CRAN
Description: Spatial models in gamlss
Author: Fernanda De Bastiani, Mikis Stasinopoulos,
Maintainer: Fernanda De Bastiani
DESCRIPTION | 10
MD5 | 8
NAMESPACE | 11 -
R/extraFunctions.R | 537 ++++++++++++++++++++++++++---------------------------
R/mrf-for-gamlss.R | 5
5 files changed, 287 insertions(+), 284 deletions(-)
Permanent link
Title: Probabilistic Population Projection
Diff between bayesPop versions 5.2-1 dated 2014-11-20 and 5.2-2 dated 2015-02-05
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
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/get_outputs.R | 4 ++--
man/bayesPop-package.Rd | 7 ++++---
5 files changed, 18 insertions(+), 13 deletions(-)