Title: Estimate permutation p-values for importance metrics.
Diff between rfPermute versions 1.0.1 dated 2011-08-24 and 1.1 dated 2012-04-26
Description: Estimate significance of importance metrics for a Random
Forest model by permuting the response variable. Produces null
distribution of importance metrics for each predictor variable
and p-value of observed.
Author: Eric Archer
Maintainer: Eric Archer
DESCRIPTION | 12 +--
MD5 | 16 ++--
NAMESPACE | 10 +-
R/plot.rfPermute.R | 94 +++++++++++++-----------
R/rfPermute.R | 130 ++++++++++++++++-----------------
R/rfPermute.default.R | 175 +++++++++++++++++++++++----------------------
R/rfPermute.formula.R | 123 +++++++++++++++----------------
man/plot.rfPermute.Rd | 59 ++++++++-------
man/rfPermute.Rd | 193 ++++++++++++++++++++++++--------------------------
9 files changed, 416 insertions(+), 396 deletions(-)
Title: Estimation of CPDAG/PAG and causal inference using the IDA
algorithm
Diff between pcalg versions 1.1-4 dated 2011-05-09 and 1.1-5 dated 2012-04-26
Description: Standard and robust estimation of the equivalence class of
a Directed Acyclic Graph (DAG) via the PC-Algorithm. The
equivalence class is represented by its (unique) Completete
Partially Directed Acyclic Graph (CPDAG). Furthermore, a PAG
instead of a CPDAG can be estimated if latent variables and/or
selection variables are assumed to be present. FCI and RFCI are
available for estimating PAGs. Functions for causal inference
using the IDA algorithm (based on do-calculus of Judea Pearl)
are provided for CPDAGs.
Author: Markus Kalisch, Martin Maechler, Diego Colombo
Maintainer: Markus Kalisch
pcalg-1.1-4/pcalg/bugs |only
pcalg-1.1-4/pcalg/inst/doc/Makefile |only
pcalg-1.1-4/pcalg/inst/doc/auto |only
pcalg-1.1-4/pcalg/inst/doc/changes |only
pcalg-1.1-4/pcalg/inst/doc/jss.bst |only
pcalg-1.1-4/pcalg/inst/doc/jss.cls |only
pcalg-1.1-4/pcalg/inst/doc/jssStyle |only
pcalg-1.1-4/pcalg/inst/doc/lmPlot.pdf |only
pcalg-1.1-4/pcalg/inst/doc/lmPlot2.pdf |only
pcalg-1.1-4/pcalg/inst/doc/seedTest.R |only
pcalg-1.1-5/pcalg/DESCRIPTION | 8
pcalg-1.1-5/pcalg/MD5 |only
pcalg-1.1-5/pcalg/R/pcalg.R | 6
pcalg-1.1-5/pcalg/data/datalist |only
pcalg-1.1-5/pcalg/inst/CITATION |only
pcalg-1.1-5/pcalg/inst/doc/Figure1FAT.pdf |only
pcalg-1.1-5/pcalg/inst/doc/Mybib.bib | 154 +++-
pcalg-1.1-5/pcalg/inst/doc/pcalgDoc.Rnw | 1003 +++++++++++++++++-------------
pcalg-1.1-5/pcalg/inst/doc/pcalgDoc.pdf |binary
pcalg-1.1-5/pcalg/man/fci.Rd | 5
pcalg-1.1-5/pcalg/man/ida.Rd | 8
pcalg-1.1-5/pcalg/man/idaFast.Rd | 5
pcalg-1.1-5/pcalg/man/pc.Rd | 5
23 files changed, 741 insertions(+), 453 deletions(-)
Title: A Laboratory for Recursive Partytioning
Diff between party versions 1.0-1 dated 2012-03-23 and 1.0-2 dated 2012-04-26
Description: A computational toolbox for recursive partitioning. The
core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems,
including nominal, ordinal, numeric, censored as well as
multivariate response variables and arbitrary measurement
scales of the covariates. Based on conditional inference
trees, cforest() provides an implementation of Breiman's random
forests. The function mob() implements an algorithm for
recursive partitioning based on parametric models (e.g. linear
models, GLMs or survival regression) employing parameter
instability tests for split selection. Extensible functionality
for visualizing tree-structured regression models is available.
Author: Torsten Hothorn [aut, cre], Kurt Hornik [aut], Carolin Strobl
[aut], Achim Zeileis [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
R/Classes.R | 2 +-
R/Plot.R | 4 ++--
R/RandomForest.R | 2 +-
data/mammoexp.rda |binary
inst/NEWS | 7 +++++++
inst/doc/MOB.pdf |binary
inst/doc/party.pdf |binary
tests/bugfixes.Rout.save | 7 ++++---
tests/mob.Rout.save | 18 ++++++++++--------
vignettes/MOB.Rout.save | 21 +--------------------
12 files changed, 41 insertions(+), 50 deletions(-)
Title: Variable selection for generalized linear mixed models by
L1-penalized estimation
Diff between glmmLasso versions 1.0.1 dated 2012-03-29 and 1.0.2 dated 2012-04-26
Description: Variable selection for generalized linear mixed models by
L1-penalized estimation
Author: Andreas Groll
Maintainer: Andreas Groll
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/glmmLasso.r | 53 ++++++++++++++++++++++++++++++++++++-----------------
R/glmm_final.r | 6 +++---
man/glmmLasso.rd | 4 ++--
5 files changed, 49 insertions(+), 30 deletions(-)
Title: Financial Risk Management and Quantitative Analysis
Diff between frmqa versions 0.1-0 dated 2012-04-17 and 0.1-1 dated 2012-04-26
Description: R and C++ functions for financial risk management and
quantative analysis, using the generalized perbolic and its
related distributions.
Author: Thanh T. Tran
Maintainer: Thanh T. Tran
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
man/besselK_app_ser.Rd | 2 +-
man/besselK_inc_clo.Rd | 2 +-
man/frmqa-package.Rd | 4 ++--
5 files changed, 12 insertions(+), 12 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-17 dated 2012-02-08 and 7.3-18 dated 2012-04-26
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Kurt Hornik [trl] (partial port
ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David
Firth [ctb]
Maintainer: Brian Ripley
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
R/boxcox.R | 13 ++++++-------
R/isoMDS.R | 4 +++-
inst/NEWS | 4 +++-
src/lqs.c | 2 +-
6 files changed, 23 insertions(+), 20 deletions(-)
Title: Bayesian Instrumental Variable Estimation and Model
Determination via Conditional Bayes Factors
Diff between ivbma versions 1.01 dated 2012-03-19 and 1.02 dated 2012-04-26
Description: This package allows one incorporate instrument and
covariate uncertainty into instrumental variable regression.
Author: Alex Lenkoski, Anna Karl, Andreas Neudecker
Maintainer: Alex Lenkoski
DESCRIPTION | 6 +++---
MD5 | 7 ++++---
NAMESPACE | 1 +
R/dynamic.probit.R |only
R/ivbma.R | 27 +++++++++++++++++++++++++--
5 files changed, 33 insertions(+), 8 deletions(-)
Title: Fitting Single and Mixture of Generalised Lambda Distributions
(RS and FMKL) using Various Methods
Diff between GLDEX versions 1.0.4.3 dated 2012-03-08 and 1.0.4.4 dated 2012-04-26
Description: The fitting algorithms considered in this package have two
major objectives. One is to provide a smoothing device to fit
distributions to data using the weight and unweighted
discretised approach based on the bin width of the histogram.
The other is to provide a definitive fit to the data set using
the maximum likelihood and quantile matching estimation. Other
methods such as moment matching, starship method, L moment
matching are also provided. Diagnostics on goodness of fit can
be done via qqplots, KS-resample tests and comparing mean,
variance, skewness and kurtosis of the data with the fitted
distribution.
Author: Steve Su, Diethelm Wuertz and Rmetrics core team members for
low discrepancy algorithm, Robert King for gld C codes,
Benjamin Dean for corrections and input in ks.gof code
Maintainer: Steve Su
DESCRIPTION | 8
MD5 | 4
src/085A-LowDiscrepancy.f | 924 ++++++++++++++++++++++++----------------------
3 files changed, 496 insertions(+), 440 deletions(-)
Title: Diversity-dependent diversification
Diff between DDD versions 0.4 dated 2012-02-08 and 1.1 dated 2012-04-26
Description: DDD implements maximum likelihood methods based on the
diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent. See Etienne
et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi:
10.1098/rspb.2011.1439. DDD also implements a maximum
likelihood method to detect key innovations defined as
decoupling of diversity-dependence. See Etienne & Haegeman
2012, Am. Nat. In press.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne
DESCRIPTION | 14 +++++++++-----
MD5 | 35 +++++++++++++++++++++--------------
R/dd_KI_ML.R |only
R/dd_KI_loglik.R |only
R/dd_KI_loglik_choosepar.R |only
R/dd_ML.R | 13 +++++++++----
R/dd_SR_ML.R | 8 +++++---
R/dd_SR_loglik.R | 10 ++++++----
R/dd_SR_loglik_choosepar.R | 2 +-
R/dd_loglik.R | 24 +++++++++++++++---------
R/dd_loglik_choosepar.R | 3 ++-
R/dd_loglik_rhs.R | 17 ++++++++++++++---
R/dd_logliknorm_rhs1.R |only
R/dd_logliknorm_rhs2.R |only
man/DDD-internal.Rd | 5 +++--
man/DDD-package.Rd | 33 ++++++++++++++++++++++++++++-----
man/dd_KI_ML.Rd |only
man/dd_KI_loglik.Rd |only
man/dd_ML.Rd | 17 +++++++++++------
man/dd_SR_ML.Rd | 17 ++++++++++-------
man/dd_SR_loglik.Rd | 20 ++++++++------------
man/dd_loglik.Rd | 8 +++++---
22 files changed, 147 insertions(+), 79 deletions(-)