Author: Chris Stubben, Brook Milligan, Patrick Nantel
Title: Construction and analysis of matrix population models
Description: Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).
Diff between popbio versions 1.1.8 dated 2008-03-14 and 1.1.9 dated 2008-07-16
popbio-1.1.8/popbio/data/hudcorrs.R |only popbio-1.1.8/popbio/inst/doc |only popbio-1.1.9/popbio/DESCRIPTION | 6 +-- popbio-1.1.9/popbio/R/multiresultm.R | 2 - popbio-1.1.9/popbio/R/projection.matrix.R | 11 +++-- popbio-1.1.9/popbio/R/vitalsens.R | 2 - popbio-1.1.9/popbio/data/hudcorrs.rda |only popbio-1.1.9/popbio/inst/._CITATION |only popbio-1.1.9/popbio/inst/CITATION |only popbio-1.1.9/popbio/inst/ChangeLog |only popbio-1.1.9/popbio/man/01Introduction.Rd | 7 ++- popbio-1.1.9/popbio/man/02Caswell.Rd | 9 ++++ popbio-1.1.9/popbio/man/boot.transitions.Rd | 50 ++++++++----------------- popbio-1.1.9/popbio/man/extCDF.Rd | 3 - popbio-1.1.9/popbio/man/hudcorrs.Rd | 4 -- popbio-1.1.9/popbio/man/multiresultm.Rd | 12 +++--- popbio-1.1.9/popbio/man/projection.matrix.Rd | 53 ++++++++++++--------------- popbio-1.1.9/popbio/man/teasel.Rd | 2 - popbio-1.1.9/popbio/man/test.census.Rd | 24 ++++++------ popbio-1.1.9/popbio/man/vitalsens.Rd | 6 +-- popbio-1.1.9/popbio/man/woodpecker.Rd | 4 ++ 21 files changed, 97 insertions(+), 98 deletions(-)
Author: Aaron A. King, Edward L. Ionides, Carles Martinez Breto
Title: Partially-observed Markov processes
Description: Inference methods for partially-observed Markov processes
Diff between pomp versions 0.19-1 dated 2008-05-19 and 0.20-2 dated 2008-07-16
pomp-0.19-1/pomp/R/print-pomp.R |only pomp-0.19-1/pomp/inst/include/euler.h |only pomp-0.19-1/pomp/inst/include/lookup_table.h |only pomp-0.19-1/pomp/src/euler.h |only pomp-0.19-1/pomp/src/lookup_table.h |only pomp-0.20-2/pomp/DESCRIPTION | 6 pomp-0.20-2/pomp/NAMESPACE | 20 - pomp-0.20-2/pomp/R/aaa.R | 100 +++++ pomp-0.20-2/pomp/R/compare.mif.R |only pomp-0.20-2/pomp/R/dmeasure-pomp.R | 12 pomp-0.20-2/pomp/R/euler.R | 60 ++- pomp-0.20-2/pomp/R/init.state-pomp.R | 1 pomp-0.20-2/pomp/R/mif-methods.R | 26 + pomp-0.20-2/pomp/R/mif.R | 25 + pomp-0.20-2/pomp/R/plot-pomp.R | 12 pomp-0.20-2/pomp/R/pomp-methods.R | 49 ++ pomp-0.20-2/pomp/R/pomp.R | 288 +++++++++++++++-- pomp-0.20-2/pomp/R/rmeasure-pomp.R | 12 pomp-0.20-2/pomp/R/simulate-pomp.R | 5 pomp-0.20-2/pomp/R/skeleton-pomp.R |only pomp-0.20-2/pomp/data/ou2.rda |binary pomp-0.20-2/pomp/inst/ChangeLog |only pomp-0.20-2/pomp/inst/NEWS |only pomp-0.20-2/pomp/inst/doc/compiled_code_in_pomp.Rnw | 123 ------- pomp-0.20-2/pomp/inst/doc/compiled_code_in_pomp.pdf |binary pomp-0.20-2/pomp/inst/doc/intro_to_pomp.Rnw | 87 ++--- pomp-0.20-2/pomp/inst/doc/intro_to_pomp.pdf |binary pomp-0.20-2/pomp/inst/examples/sir.R | 251 ++++++++------ pomp-0.20-2/pomp/inst/examples/sir.c | 104 ++++-- pomp-0.20-2/pomp/inst/include/pomp.h |only pomp-0.20-2/pomp/man/dmeasure-pomp.Rd | 5 pomp-0.20-2/pomp/man/dprocess-pomp.Rd | 88 ++--- pomp-0.20-2/pomp/man/euler.Rd | 154 +++------ pomp-0.20-2/pomp/man/eulermultinom.Rd | 2 pomp-0.20-2/pomp/man/mif-class.Rd | 15 pomp-0.20-2/pomp/man/mif-methods.Rd | 25 + pomp-0.20-2/pomp/man/mif.Rd | 5 pomp-0.20-2/pomp/man/pomp-class.Rd | 109 +----- pomp-0.20-2/pomp/man/pomp-methods.Rd |only pomp-0.20-2/pomp/man/pomp.Rd | 142 +++++--- pomp-0.20-2/pomp/man/rmeasure-pomp.Rd | 38 +- pomp-0.20-2/pomp/man/skeleton-pomp.Rd |only pomp-0.20-2/pomp/src/bspline.c | 2 pomp-0.20-2/pomp/src/dmeasure.c | 259 +++++++++++++-- pomp-0.20-2/pomp/src/dprocess.c | 32 + pomp-0.20-2/pomp/src/dsobol.c | 2 pomp-0.20-2/pomp/src/euler.c | 336 ++++++++++++++++---- pomp-0.20-2/pomp/src/eulermultinom.c | 2 pomp-0.20-2/pomp/src/initstate.c | 47 ++ pomp-0.20-2/pomp/src/lookup_table.c | 49 ++ pomp-0.20-2/pomp/src/ou2.c | 200 ++--------- pomp-0.20-2/pomp/src/pomp.h | 228 ++++++++----- pomp-0.20-2/pomp/src/pomp_fun.c |only pomp-0.20-2/pomp/src/pomp_internal.h |only pomp-0.20-2/pomp/src/resample.c | 2 pomp-0.20-2/pomp/src/rmeasure.c | 249 ++++++++++++-- pomp-0.20-2/pomp/src/rprocess.c | 30 + pomp-0.20-2/pomp/src/sir.c | 104 ++++-- pomp-0.20-2/pomp/src/skeleton.c |only pomp-0.20-2/pomp/tests/ou2-kalman.R | 18 - pomp-0.20-2/pomp/tests/ou2-kalman.Rout.save |only pomp-0.20-2/pomp/tests/ou2-mif.R | 22 - pomp-0.20-2/pomp/tests/ou2-mif.Rout.save |only pomp-0.20-2/pomp/tests/ou2-simulate.Rout.save |only pomp-0.20-2/pomp/tests/rw2.R | 137 +++++--- pomp-0.20-2/pomp/tests/rw2.Rout.save |only pomp-0.20-2/pomp/tests/sir.R |only pomp-0.20-2/pomp/tests/sir.Rout.save |only 68 files changed, 2287 insertions(+), 1196 deletions(-)
Author: Simon Jackman, with contributions from
Alex Tahk, Achim Zeileis, Christina Maimone and Jim Fearon
Title: Political Science Computational Laboratory, Stanford University
Description: Bayesian analysis of item-response theory (IRT) models, roll call analysis;
computing highest density regions; maximum likelihood estimation of
zero-inflated and hurdle models for count data; goodness-of-fit measures for
GLMs; data sets used in writing and teaching at the Political Science
Computational Laboratory; seats-votes curves.
Diff between pscl versions 0.96 dated 2008-06-26 and 0.97 dated 2008-07-16
DESCRIPTION | 6 - HISTORY | 9 ++ R/dropRollCall.r | 157 ++++++++++++++++++++++++++++++++--------- R/ideal.r | 10 ++ R/igamma.r | 20 +++-- R/margins.rollcall.r | 3 R/plot.ideal.r | 8 +- R/postProcess.r | 33 ++++---- R/rollcall.r | 114 +++++++++++++++++++++-------- R/summary.ideal.r | 34 ++++++-- data/presidentialElections.rda |only data/s109.rda |binary inst/doc/.build.timestamp |only inst/doc/auto/countreg.el | 17 +--- inst/doc/countreg.pdf |binary man/dropRollCall.Rd | 66 +++++++++++++---- man/dropUnanimous.Rd | 2 man/hitmiss.Rd | 3 man/idealToMCMC.Rd | 5 - man/plot.ideal.Rd | 7 + man/presidentialElections.Rd |only man/readKH.Rd | 5 - man/s109.Rd | 38 +++++---- man/simpi.Rd | 4 - man/summary.rollcall.Rd | 6 + 25 files changed, 388 insertions(+), 159 deletions(-)
Author: Kaspar Rufibach
Diff between logcondens versions 1.3.1 dated 2007-10-04 and 1.3.2 dated 2008-07-16
Title: Estimate a Log-Concave Probability Density from iid Observations
Description: Given independent and identically distributed observations X(1), ..., X(n), this package allows to
compute a concave, piecewise linear function phi on [X(1), X(n)] with knots only in {X(1), X(2), ..., X(n)}
such that L(phi) = sum_{i=1}^n W(i)*phi(X(i)) - int_{X(1)}^{X(n)} exp(phi(x)) dx is maximal, for some
weights W(1), ..., W(n) s.t. sum_{i=1}^n W(i) = 1. According to the results in Duembgen and Rufibach (2008),
this function phi maximizes the ordinary log-likelihood sum_{i=1}^n W(i)*phi(X(i))
under the constraint that phi is concave. The corresponding function exp(phi) is a log-concave probability density.
Two algorithms are offered: An active set algorithm and one based on the pool-adjacent-violaters algorithm.
DESCRIPTION | 14
R/intF.r | 4
inst/doc/logcondens_vignette.pdf | 751 +++++++++++++++++++--------------------
man/Jfunctions.Rd | 4
man/Lhat_eta.Rd | 4
man/Local_LL.Rd | 4
man/Local_LL_all.Rd | 4
man/MLE.Rd | 4
man/activeSetLogCon.Rd | 12
man/activeSetRoutines.Rd | 4
man/evaluateLogConDens.Rd | 4
man/icmaLogCon.Rd | 4
man/intECDF.Rd | 10
man/intF.Rd | 16
man/isoMean.Rd | 4
man/logcondens-package.Rd | 22 -
man/qloglin.Rd | 4
man/quadDeriv.Rd | 4
man/quantilesLogConDens.Rd | 4
man/reparametrizations.Rd | 4
man/robust.Rd | 4
21 files changed, 447 insertions(+), 438 deletions(-)
Author: Michel Grabisch, Ivan Kojadinovic, Patrick Meyer.
Title: Non-additive measure and integral manipulation functions
Description: Kappalab, which stands for "laboratory for capacities", is an S4 tool box for capacity (or non-additive measure, fuzzy measure) and integral manipulation on a finite setting. It contains routines for handling various types of set functions such as games or capacities. It can be used to compute several non-additive integrals: the Choquet integral, the Sugeno integral, and the symmetric and asymmetric Choquet integrals. An analysis of capacities in terms of decision behavior can be performed through the computation of various indices such as the Shapley value, the interaction index, the orness degree, etc. The well-known Möbius transform, as well as other equivalent representations of set functions can also be computed. Kappalab further contains seven capacity identification routines: three least squares based approaches, a method based on linear programming, a maximum entropy like method based on variance minimization, a minimum distance approach and an unsupervised approach grounded on parametric entropies. The functions contained in Kappalab can for instance be used in the framework of multicriteria decision making or cooperative game theory.
Diff between kappalab versions 0.4-1 dated 2007-12-07 and 0.4-3 dated 2008-07-16
kappalab-0.4-1/kappalab/man/round-methods.Rd |only kappalab-0.4-3/kappalab/DESCRIPTION | 6 +++--- kappalab-0.4-3/kappalab/NAMESPACE | 2 +- kappalab-0.4-3/kappalab/R/AllGeneric.R | 6 +++--- kappalab-0.4-3/kappalab/R/ls.ranking.capa.ident.R | 12 +++++++++--- kappalab-0.4-3/kappalab/R/superclass.set.func.R | 2 +- kappalab-0.4-3/kappalab/man/Choquet.integral-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/Mobius-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/Mobius.capacity-class.Rd | 2 +- kappalab-0.4-3/kappalab/man/Mobius.card.set.func-class.Rd | 2 +- kappalab-0.4-3/kappalab/man/Mobius.game-class.Rd | 2 +- kappalab-0.4-3/kappalab/man/Mobius.set.func-class.Rd | 6 +++--- kappalab-0.4-3/kappalab/man/Sipos.integral-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/Sugeno.integral-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/entropy-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/favor-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/is.kadditive-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/is.monotone-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/is.normalized-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/ls.ranking.capa.ident.Rd | 2 +- kappalab-0.4-3/kappalab/man/rnd-methods.Rd |only kappalab-0.4-3/kappalab/man/show-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/superclass.set.func-class.Rd | 6 +++--- kappalab-0.4-3/kappalab/man/to.data.frame-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/variance-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/veto-methods.Rd | 2 +- kappalab-0.4-3/kappalab/man/zeta-methods.Rd | 2 +- kappalab-0.4-3/kappalab/src/core.c | 4 ++++ 28 files changed, 45 insertions(+), 35 deletions(-)
Author: R-core members, Saikat DebRoy
Diff between foreign versions 0.8-26 dated 2008-05-29 and 0.8-27 dated 2008-07-16
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ...
Description: Functions for reading and writing data stored by statistical
packages such as Minitab, S, SAS, SPSS, Stata, Systat, ...,
and for reading and writing .dbf (dBase) files.
ChangeLog | 43 ++++--
DESCRIPTION | 6
K_Van_Dijck_patch |only
K_Van_Dijck_patch-2 |only
src/SASxport.c | 7 -
src/minitab.c | 5
src/sfm-read.c | 72 ++++++++++-
src/sfm-read.c.orig |only
src/sfm-read.c.rej |only
src/spss.c | 5
src/stataread.c | 7 -
src/var.h.in | 12 +
src/var.h.in.orig |only
src/var.h.in.rej |only
tests/sas.R | 1
tests/spss.R | 70 +++++++---
tests/spss.Rout.save | 326 ++++++++-------------------------------------------
tests/spss_long.sav |only
18 files changed, 230 insertions(+), 324 deletions(-)
Author: Chandra Erdman and John W. Emerson
Title: A Package for Performing a Bayesian Analysis of Change Point Problems
Description: An implementation of the Barry and Hartigan (1993) product partition model for the standard change point problem using Markov Chain Monte Carlo.
Diff between bcp versions 2.0 dated 2008-06-01 and 2.1 dated 2008-07-16
DESCRIPTION | 23 +++--- NAMESPACE | 2 R/bcp.R | 88 ++++++++++++++++++++++++- R/output.R | 5 + man/RealInt.Rd | 39 ++++++----- man/bcp.Rd | 142 +++++++++++++++++++++++++---------------- man/coriell.Rd | 107 ++++++++++++++++--------------- man/fitted.bcp.Rd | 150 +++++++++++-------------------------------- man/interval.prob.Rd |only man/plot.bcp.Rd | 154 ++++++++++++--------------------------------- man/print.bcp.Rd | 170 +++++++++++++++---------------------------------- man/residuals.bcp.Rd | 149 +++++++++++-------------------------------- man/summary.bcp.Rd | 174 ++++++++++++++++----------------------------------- 13 files changed, 496 insertions(+), 707 deletions(-)
Author: A.I. McLeod and Ying Zhang
Title: Subset AR Model Fitting
Description: Complete functions are given for model identification, estimation and diagnostic checking for AR and subset AR models. Two types of subset AR models are supported. One family of subset AR models, denoted by ARp, is formed by taking subet of the original AR coefficients and in the other, denoted by ARz, subsets of the partial autocorrelations are used. The main advantage of the ARz model is its applicability to very large order models.
Diff between FitAR versions 1.7 dated 2008-06-25 and 1.71 dated 2008-07-16
DESCRIPTION | 6 +++--- R/cts.R | 6 +++++- man/FitAR-package.Rd | 4 ++-- man/cts.Rd | 36 +++++++++++++++++++++++++++++++++--- 4 files changed, 43 insertions(+), 9 deletions(-)
Author: Andreas Kiermeier
Diff between AcceptanceSampling versions 0.1-4 dated 2008-05-16 and 1.0-0 dated 2008-07-16
More information about AcceptanceSampling at CRAN
Title: Creation and evaluation of Acceptance Sampling Plans
Description: This package provides functionality for creating and
evaluating acceptance sampling plans. Plans can be single,
double or multiple sampling plans
DESCRIPTION | 4 ++--
inst |only
2 files changed, 2 insertions(+), 2 deletions(-)
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