Title: Time Dependent Point Process Modelling
Diff between PtProcess versions 3.3-7 dated 2014-10-16 and 3.3-9 dated 2015-04-12
Description: Fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Change Log".
Author: David Harte
Maintainer: David Harte
DESCRIPTION | 11 +++++------
MD5 | 14 +++++++-------
R/logLik.mpp.R | 2 +-
data/NthChina.rda |binary
data/Ogata.rda |binary
data/Phuket.rda |binary
data/Tangshan.rda |binary
man/Changes.Rd | 4 +++-
8 files changed, 16 insertions(+), 15 deletions(-)
Title: Hidden Markov Models
Diff between HiddenMarkov versions 1.8-1 dated 2014-09-25 and 1.8-3 dated 2015-04-12
Description: Contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. See the topic "HiddenMarkov" for an introduction to the package, and "Change Log" for a list of recent changes. The algorithms are based of those of Walter Zucchini.
Author: David Harte
Maintainer: David Harte
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
inst/CITATION | 11 +++++------
man/Changes.Rd | 2 ++
man/HiddenMarkov.Rd | 2 +-
5 files changed, 16 insertions(+), 15 deletions(-)
Title: Resampling Functions
Diff between resample versions 0.2 dated 2014-03-12 and 0.4 dated 2015-04-12
Description: Bootstrap, permutation tests, and other resampling functions,
featuring easy-to-use syntax.
Author: Tim Hesterberg
Maintainer: Tim Hesterberg
resample-0.2/resample/R/anyNA.R |only
resample-0.2/resample/R/cat.R |only
resample-0.2/resample/src |only
resample-0.4/resample/DESCRIPTION | 14 -
resample-0.4/resample/MD5 | 64 ++++----
resample-0.4/resample/NAMESPACE | 25 ++-
resample-0.4/resample/R/BootStats.R | 29 +++
resample-0.4/resample/R/MakeFunction.R | 12 -
resample-0.4/resample/R/SetSeed.R | 4
resample-0.4/resample/R/bootstrap.R | 40 ++---
resample-0.4/resample/R/bootstrap2.R | 137 ++++++++++-------
resample-0.4/resample/R/cat0.R |only
resample-0.4/resample/R/jackknife.R |only
resample-0.4/resample/R/limits.R | 160 +++++++++++++++++++-
resample-0.4/resample/R/permutationTest.R | 44 ++---
resample-0.4/resample/R/permutationTest2.R | 110 +++++++-------
resample-0.4/resample/R/resample.R | 140 ++++++++++++-----
resample-0.4/resample/R/samplers.R | 65 ++++++--
resample-0.4/resample/data |only
resample-0.4/resample/inst |only
resample-0.4/resample/man/ExpandProbs.Rd |only
resample-0.4/resample/man/IfElse.Rd |only
resample-0.4/resample/man/Quantile.Rd |only
resample-0.4/resample/man/bootstrap.Rd | 71 +++++----
resample-0.4/resample/man/cat0.Rd |only
resample-0.4/resample/man/colVars.Rd |only
resample-0.4/resample/man/deprecated.Rd |only
resample-0.4/resample/man/jackknife.Rd |only
resample-0.4/resample/man/limits.percentile.Rd | 60 ++++++-
resample-0.4/resample/man/print.resample.Rd | 99 ++++++++----
resample-0.4/resample/man/resample-data.Rd |only
resample-0.4/resample/man/resample-package.Rd | 195 +++++++++++++++++++++++--
resample-0.4/resample/man/resample.Rd | 40 +++--
resample-0.4/resample/man/samp.bootstrap.Rd | 13 -
resample-0.4/resample/tests/bootstrap.t | 37 ++--
resample-0.4/resample/tests/bootstrap2.t | 60 ++++---
resample-0.4/resample/tests/confidence.t |only
resample-0.4/resample/tests/jackknife.t |only
resample-0.4/resample/tests/permutationTest.t | 58 +++++--
resample-0.4/resample/tests/permutationTest2.t | 79 ++++++----
resample-0.4/resample/tests/samplers.t | 44 ++---
41 files changed, 1111 insertions(+), 489 deletions(-)
Title: Analysis of Queueing Networks and Models
Diff between queueing versions 0.2.3 dated 2014-12-07 and 0.2.4 dated 2015-04-12
Description: It provides versatile tools for analysis of birth and death based Markovian Queueing Models
and Single and Multiclass Product-Form Queueing Networks.
It implements M/M/1, M/M/c, M/M/Infinite, M/M/1/K, M/M/c/K, M/M/c/c, M/M/1/K/K, M/M/c/K/K, M/M/c/K/m, M/M/Infinite/K/K,
Multiple Channel Open Jackson Networks, Multiple Channel Closed Jackson Networks,
Single Channel Multiple Class Open Networks, Single Channel Multiple Class Closed Networks
and Single Channel Multiple Class Mixed Networks.
Also it provides a B-Erlang, C-Erlang and Engset calculators.
This work is dedicated to the memory of D. Sixto Rios Insua.
Author: Pedro Canadilla
Maintainer: Pedro Canadilla
ChangeLog | 3 +++
DESCRIPTION | 19 +++++++++++++------
MD5 | 6 +++---
inst/CITATION | 25 ++++++++-----------------
4 files changed, 27 insertions(+), 26 deletions(-)
Title: Data Sets from Montgomery, Peck and Vining's Book
Diff between MPV versions 1.35 dated 2014-09-03 and 1.38 dated 2015-04-12
Description: Most of this package consists of data sets from the
textbook Introduction
to Linear Regression Analysis (3rd ed), by Montgomery et al.
Some additional data sets and functions useful in an
undergraduate regression course are included.
Author: W.J. Braun
Maintainer: W.J. Braun
DESCRIPTION | 6 +++---
MD5 | 16 +++++++++++-----
R/GANOVA.R |only
R/Qyplot.R | 2 +-
R/Uplot.R | 4 ++--
data/Juliet.rda |only
data/oldwash.rda |only
data/pathoeg.rda |binary
man/GANOVA.Rd |only
man/Juliet.Rd |only
man/Uplot.Rd | 3 ++-
man/oldwash.Rd |only
12 files changed, 19 insertions(+), 12 deletions(-)
Title: Interface Utilities, Model Templates, Parallel Computing Methods
and Additional Distributions for MCMC Models in JAGS
Diff between runjags versions 1.2.1-0 dated 2014-06-21 and 2.0.1-2 dated 2015-04-12
Description: User-friendly interface utilities for MCMC models via
Just Another Gibbs Sampler (JAGS), facilitating the use of parallel
(or distributed) processors for multiple chains, automated control
of convergence and sample length diagnostics, and evaluation of the
performance of a model using drop-k validation or against simulated
data. Template model specifications can be generated using a standard
lme4-style formula interface to assist users less familiar with the
BUGS syntax. A JAGS extension module provides additional distributions
including the Pareto family of distributions, the DuMouchel prior and
the half-Cauchy prior.
Author: Matthew Denwood [aut, cre],
Martyn Plummer [cph] (Copyright holder of the code in
/src/distributions/jags, src/distributions/DPar1.*, configure.ac,
and original copyright holder of some modified code where
indicated)
Maintainer: Matthew Denwood
runjags-1.2.1-0/runjags/R/autorun.run.jags.file.R |only
runjags-1.2.1-0/runjags/R/read.winbugs.R |only
runjags-1.2.1-0/runjags/inst/doc/module_distributions.pdf |only
runjags-1.2.1-0/runjags/inst/doc/runjags.Rtex |only
runjags-1.2.1-0/runjags/inst/doc/runjags.pdf |only
runjags-1.2.1-0/runjags/man/jagsfile.Rd |only
runjags-1.2.1-0/runjags/man/load.module.runjags.Rd |only
runjags-1.2.1-0/runjags/man/read.winbugs.Rd |only
runjags-1.2.1-0/runjags/src/distributions/DHCauchy.cc |only
runjags-1.2.1-0/runjags/src/distributions/DHCauchy.h |only
runjags-1.2.1-0/runjags/vignettes/runjags.Rtex |only
runjags-2.0.1-2/runjags/CHANGELOG | 83
runjags-2.0.1-2/runjags/DESCRIPTION | 49
runjags-2.0.1-2/runjags/MD5 | 130
runjags-2.0.1-2/runjags/NAMESPACE | 71
runjags-2.0.1-2/runjags/R/autoextend.jags.R | 942 +---
runjags-2.0.1-2/runjags/R/combine.mcmc.R | 155
runjags-2.0.1-2/runjags/R/dump.list.format.R | 42
runjags-2.0.1-2/runjags/R/extend.jags.R | 881 +++-
runjags-2.0.1-2/runjags/R/extract.runjags.R |only
runjags-2.0.1-2/runjags/R/load.module.runjags.R | 136
runjags-2.0.1-2/runjags/R/mutate.functions.R |only
runjags-2.0.1-2/runjags/R/print.methods.R | 487 --
runjags-2.0.1-2/runjags/R/read.jagsfile.R |only
runjags-2.0.1-2/runjags/R/results.jags.R |only
runjags-2.0.1-2/runjags/R/run.jags.study.R | 658 ++-
runjags-2.0.1-2/runjags/R/runjags.readin.R | 681 ++-
runjags-2.0.1-2/runjags/R/runjags.start.R | 2957 ++++++++------
runjags-2.0.1-2/runjags/R/runjags.summaries.R | 639 ++-
runjags-2.0.1-2/runjags/R/runjagsclass.R |only
runjags-2.0.1-2/runjags/R/setup.jags.jagsfile.R | 778 ++-
runjags-2.0.1-2/runjags/R/summary.R |only
runjags-2.0.1-2/runjags/R/template.jags.R |only
runjags-2.0.1-2/runjags/R/utilities.R | 1151 ++---
runjags-2.0.1-2/runjags/R/utilities.invisible.R | 1345 +++++-
runjags-2.0.1-2/runjags/R/xgrid.run.R | 2
runjags-2.0.1-2/runjags/R/xgrid.run.jags.R | 232 -
runjags-2.0.1-2/runjags/R/xgrid.utilities.R | 26
runjags-2.0.1-2/runjags/R/zzz.R | 21
runjags-2.0.1-2/runjags/build/vignette.rds |binary
runjags-2.0.1-2/runjags/inst/CITATION | 10
runjags-2.0.1-2/runjags/inst/doc/UserGuide.Rtex |only
runjags-2.0.1-2/runjags/inst/doc/UserGuide.pdf |only
runjags-2.0.1-2/runjags/inst/doc/quickjags.R |only
runjags-2.0.1-2/runjags/inst/doc/quickjags.Rmd |only
runjags-2.0.1-2/runjags/inst/doc/quickjags.html |only
runjags-2.0.1-2/runjags/inst/xgrid/beep.bat |only
runjags-2.0.1-2/runjags/man/add.summary.Rd |only
runjags-2.0.1-2/runjags/man/ask.Rd | 8
runjags-2.0.1-2/runjags/man/autorun.jags.Rd | 458 --
runjags-2.0.1-2/runjags/man/combine.mcmc.Rd | 96
runjags-2.0.1-2/runjags/man/extract.runjags.Rd |only
runjags-2.0.1-2/runjags/man/findjags.Rd | 2
runjags-2.0.1-2/runjags/man/list.dump.format.Rd | 11
runjags-2.0.1-2/runjags/man/load.runjagsmodule.Rd |only
runjags-2.0.1-2/runjags/man/mutate.functions.Rd |only
runjags-2.0.1-2/runjags/man/new_unique.Rd | 2
runjags-2.0.1-2/runjags/man/read.jagsfile.Rd |only
runjags-2.0.1-2/runjags/man/results.jags.Rd |only
runjags-2.0.1-2/runjags/man/run.jags.Rd | 516 --
runjags-2.0.1-2/runjags/man/run.jags.study.Rd | 208
runjags-2.0.1-2/runjags/man/runjags-class.Rd | 271 -
runjags-2.0.1-2/runjags/man/runjags.Rd | 98
runjags-2.0.1-2/runjags/man/runjags.options.Rd | 131
runjags-2.0.1-2/runjags/man/runjags.printmethods.Rd |only
runjags-2.0.1-2/runjags/man/template.jags.Rd |only
runjags-2.0.1-2/runjags/man/testjags.Rd | 11
runjags-2.0.1-2/runjags/man/timestring.Rd | 4
runjags-2.0.1-2/runjags/man/write.jagsfile.Rd |only
runjags-2.0.1-2/runjags/man/xgrid.run.Rd | 107
runjags-2.0.1-2/runjags/man/xgrid.run.jags.Rd | 97
runjags-2.0.1-2/runjags/src/Makevars.in | 4
runjags-2.0.1-2/runjags/src/Makevars.win | 2
runjags-2.0.1-2/runjags/src/distributions/DHalfCauchy.cc |only
runjags-2.0.1-2/runjags/src/distributions/DHalfCauchy.h |only
runjags-2.0.1-2/runjags/src/distributions/DPar4.cc | 2
runjags-2.0.1-2/runjags/src/runjags.cc | 4
runjags-2.0.1-2/runjags/src/testrunjags.cc | 4
runjags-2.0.1-2/runjags/tests/checkinputs.R | 65
runjags-2.0.1-2/runjags/tests/checkmethods.R | 97
runjags-2.0.1-2/runjags/tests/checkmodule.R | 143
runjags-2.0.1-2/runjags/tests/checkstudy.R |only
runjags-2.0.1-2/runjags/vignettes/UserGuide.Rtex |only
runjags-2.0.1-2/runjags/vignettes/quickjags.Rmd |only
runjags-2.0.1-2/runjags/vignettes/traceplots.pdf |binary
85 files changed, 8251 insertions(+), 5566 deletions(-)
Title: Fast Calculation of the Likelihood of a Stochastic Survival
Model
Diff between GUTS versions 0.4.14 dated 2015-04-03 and 0.5.2 dated 2015-04-12
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert
Maintainer: Sören Vogel
GUTS-0.4.14/GUTS/cleanup |only
GUTS-0.4.14/GUTS/configure |only
GUTS-0.4.14/GUTS/src/GUTS.cpp |only
GUTS-0.4.14/GUTS/src/GUTS.h |only
GUTS-0.4.14/GUTS/src/GUTS_calcLoglikelihood.cpp |only
GUTS-0.4.14/GUTS/src/GUTS_calcSample.cpp |only
GUTS-0.4.14/GUTS/src/GUTS_calcSurvivalProbabilities.cpp |only
GUTS-0.4.14/GUTS/src/Makevars.in |only
GUTS-0.4.14/GUTS/src/Makevars.win |only
GUTS-0.5.2/GUTS/DESCRIPTION | 16
GUTS-0.5.2/GUTS/MD5 | 18
GUTS-0.5.2/GUTS/R/GUTS.R | 30
GUTS-0.5.2/GUTS/man/Rcpp_GUTS-class.Rd | 2
GUTS-0.5.2/GUTS/src/GUTS_Rcpp.cpp | 678 +++++++++++++++-
GUTS-0.5.2/GUTS/src/GUTS_Rcpp.h |only
15 files changed, 683 insertions(+), 61 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Diff between EpiModel versions 1.1.3 dated 2015-01-18 and 1.1.4 dated 2015-04-12
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Li Wang [ctb]
Maintainer: Samuel Jenness
EpiModel-1.1.3/EpiModel/R/conc.microsim.R |only
EpiModel-1.1.3/EpiModel/R/zzz.R |only
EpiModel-1.1.3/EpiModel/inst/shiny/dcm |only
EpiModel-1.1.3/EpiModel/inst/shiny/icm |only
EpiModel-1.1.3/EpiModel/man/conc_microsim.Rd |only
EpiModel-1.1.3/EpiModel/man/get_args.Rd |only
EpiModel-1.1.3/EpiModel/man/plot.conc_microsim.Rd |only
EpiModel-1.1.4/EpiModel/DESCRIPTION | 14 -
EpiModel-1.1.4/EpiModel/MD5 | 120 +++++-----
EpiModel-1.1.4/EpiModel/NAMESPACE | 3
EpiModel-1.1.4/EpiModel/NEWS | 29 ++
EpiModel-1.1.4/EpiModel/R/EpiModel-package.r | 4
EpiModel-1.1.4/EpiModel/R/control.R | 31 +-
EpiModel-1.1.4/EpiModel/R/crosscheck.R | 53 ++--
EpiModel-1.1.4/EpiModel/R/dcm.R | 8
EpiModel-1.1.4/EpiModel/R/dcm.mods.R | 153 ++++++++-----
EpiModel-1.1.4/EpiModel/R/get.R | 46 +--
EpiModel-1.1.4/EpiModel/R/icm.R | 7
EpiModel-1.1.4/EpiModel/R/icm.mod.status.R | 4
EpiModel-1.1.4/EpiModel/R/init.R | 11
EpiModel-1.1.4/EpiModel/R/net.mod.init.R | 21 -
EpiModel-1.1.4/EpiModel/R/net.mod.status.R | 5
EpiModel-1.1.4/EpiModel/R/net.mod.vital.R | 18 -
EpiModel-1.1.4/EpiModel/R/net.utils.R | 176 ++++++++++-----
EpiModel-1.1.4/EpiModel/R/netdx.R | 15 -
EpiModel-1.1.4/EpiModel/R/netest.R | 19 -
EpiModel-1.1.4/EpiModel/R/netsim.R | 28 --
EpiModel-1.1.4/EpiModel/R/param.R | 60 +++--
EpiModel-1.1.4/EpiModel/R/plot.R | 78 ++++--
EpiModel-1.1.4/EpiModel/R/print.r | 6
EpiModel-1.1.4/EpiModel/R/saveout.R | 1
EpiModel-1.1.4/EpiModel/R/shiny.R | 4
EpiModel-1.1.4/EpiModel/R/utils.R | 62 +----
EpiModel-1.1.4/EpiModel/build/vignette.rds |binary
EpiModel-1.1.4/EpiModel/inst/doc/Intro.Rmd | 2
EpiModel-1.1.4/EpiModel/inst/doc/Intro.html | 9
EpiModel-1.1.4/EpiModel/inst/shiny/epidcm |only
EpiModel-1.1.4/EpiModel/inst/shiny/epiicm |only
EpiModel-1.1.4/EpiModel/man/EpiModel-package.Rd | 4
EpiModel-1.1.4/EpiModel/man/check_bip_degdist.Rd | 2
EpiModel-1.1.4/EpiModel/man/control.dcm.Rd | 6
EpiModel-1.1.4/EpiModel/man/control.icm.Rd | 6
EpiModel-1.1.4/EpiModel/man/control.net.Rd | 32 +-
EpiModel-1.1.4/EpiModel/man/dcm.Rd | 8
EpiModel-1.1.4/EpiModel/man/dcm.mods.Rd | 25 +-
EpiModel-1.1.4/EpiModel/man/dissolution_coefs.Rd | 77 ++++--
EpiModel-1.1.4/EpiModel/man/get_nwstats.Rd | 2
EpiModel-1.1.4/EpiModel/man/get_transmat.Rd | 2
EpiModel-1.1.4/EpiModel/man/icm.Rd | 7
EpiModel-1.1.4/EpiModel/man/init.dcm.Rd | 5
EpiModel-1.1.4/EpiModel/man/init.icm.Rd | 2
EpiModel-1.1.4/EpiModel/man/init.net.Rd | 4
EpiModel-1.1.4/EpiModel/man/netdx.Rd | 6
EpiModel-1.1.4/EpiModel/man/netest.Rd | 5
EpiModel-1.1.4/EpiModel/man/netsim.Rd | 28 --
EpiModel-1.1.4/EpiModel/man/param.dcm.Rd | 26 +-
EpiModel-1.1.4/EpiModel/man/param.icm.Rd | 23 +
EpiModel-1.1.4/EpiModel/man/param.net.Rd | 24 +-
EpiModel-1.1.4/EpiModel/man/split_bip.Rd | 2
EpiModel-1.1.4/EpiModel/tests/testthat/test-get.R | 39 +++
EpiModel-1.1.4/EpiModel/tests/testthat/test-net-long.R | 11
EpiModel-1.1.4/EpiModel/tests/testthat/test-netest.R | 44 ++-
EpiModel-1.1.4/EpiModel/tests/testthat/test-netpids.R |only
EpiModel-1.1.4/EpiModel/tests/testthat/test-netrestart.R |only
EpiModel-1.1.4/EpiModel/tests/testthat/test-utils.R |only
EpiModel-1.1.4/EpiModel/vignettes/Intro.Rmd | 2
66 files changed, 854 insertions(+), 525 deletions(-)