Author: Andrej-Nikolai Spiess
Diff between qpcR versions 1.0-6 dated 2008-02-11 and 1.1-1 dated 2008-05-14
Title: Modelling and analysis of real-time PCR data
Description: Model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).
qpcR-1.0-6/qpcR/R/expfit2.R |only
qpcR-1.0-6/qpcR/man/expfit2.Rd |only
qpcR-1.1-1/qpcR/DESCRIPTION | 12 +-
qpcR-1.1-1/qpcR/NAMESPACE | 9 +
qpcR-1.1-1/qpcR/R/AICc.R | 9 -
qpcR-1.1-1/qpcR/R/ERBCP.R |only
qpcR-1.1-1/qpcR/R/RMSE.R | 5 -
qpcR-1.1-1/qpcR/R/Rsq.R | 25 +----
qpcR-1.1-1/qpcR/R/efficiency.R | 14 ++
qpcR-1.1-1/qpcR/R/expcomp.R | 6 -
qpcR-1.1-1/qpcR/R/expfit.R | 126 +++++++++++++-------------
qpcR-1.1-1/qpcR/R/midpoint.R |only
qpcR-1.1-1/qpcR/R/modlist.R | 40 ++++----
qpcR-1.1-1/qpcR/R/onAttach.R | 5 -
qpcR-1.1-1/qpcR/R/outlier.R | 40 ++++----
qpcR-1.1-1/qpcR/R/pcrbatch.R | 159 ++++++++++++++++-----------------
qpcR-1.1-1/qpcR/R/pcrpred.R | 2
qpcR-1.1-1/qpcR/R/propagate.R |only
qpcR-1.1-1/qpcR/R/ratiocalc.R |only
qpcR-1.1-1/qpcR/R/ratiocalc.modlist.R |only
qpcR-1.1-1/qpcR/R/ratiocalc.pcrbatch.R |only
qpcR-1.1-1/qpcR/R/resVar.R | 5 -
qpcR-1.1-1/qpcR/R/sliwin.R | 5 -
qpcR-1.1-1/qpcR/man/AICc.Rd | 15 +--
qpcR-1.1-1/qpcR/man/RMSE.Rd | 11 +-
qpcR-1.1-1/qpcR/man/Rsq.Rd | 11 +-
qpcR-1.1-1/qpcR/man/confband.Rd | 2
qpcR-1.1-1/qpcR/man/evidence.Rd | 2
qpcR-1.1-1/qpcR/man/expcomp.Rd | 6 -
qpcR-1.1-1/qpcR/man/expfit.Rd | 67 ++++++++-----
qpcR-1.1-1/qpcR/man/modlist.Rd | 9 +
qpcR-1.1-1/qpcR/man/pcrbatch.Rd | 10 +-
qpcR-1.1-1/qpcR/man/pcropt1.Rd | 2
qpcR-1.1-1/qpcR/man/propagate.Rd |only
qpcR-1.1-1/qpcR/man/qpcR.Rd | 89 +++++++-----------
qpcR-1.1-1/qpcR/man/ratiocalc.Rd |only
qpcR-1.1-1/qpcR/man/resVar.Rd | 11 +-
qpcR-1.1-1/qpcR/man/sliwin.Rd | 4
38 files changed, 362 insertions(+), 339 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 0.18-2 dated 2008-05-05 and 0.18-3 dated 2008-05-14
pomp-0.18-2/pomp/inst/include/interp.h |only pomp-0.18-2/pomp/man/simulate-mif.Rd |only pomp-0.18-2/pomp/src/interp.c |only pomp-0.18-2/pomp/src/interp.h |only pomp-0.18-3/pomp/DESCRIPTION | 6 pomp-0.18-3/pomp/NAMESPACE | 6 pomp-0.18-3/pomp/R/bsplines.R | 2 pomp-0.18-3/pomp/R/dmeasure-pomp.R | 25 +- pomp-0.18-3/pomp/R/dprocess-pomp.R | 17 - pomp-0.18-3/pomp/R/euler.R | 28 ++ pomp-0.18-3/pomp/R/eulermultinom.R | 52 ---- pomp-0.18-3/pomp/R/init.state-pomp.R | 4 pomp-0.18-3/pomp/R/mif.R | 30 +- pomp-0.18-3/pomp/R/particles-mif.R | 8 pomp-0.18-3/pomp/R/pfilter.R | 26 +- pomp-0.18-3/pomp/R/plot-pomp.R | 194 ++++++++-------- pomp-0.18-3/pomp/R/pomp-methods.R | 76 +++--- pomp-0.18-3/pomp/R/pomp.R | 32 +- pomp-0.18-3/pomp/R/rmeasure-pomp.R | 20 - pomp-0.18-3/pomp/R/rprocess-pomp.R | 18 - pomp-0.18-3/pomp/R/simulate-pomp.R | 143 ++++++------ pomp-0.18-3/pomp/R/sobol.R | 4 pomp-0.18-3/pomp/data/ou2.rda |binary pomp-0.18-3/pomp/inst/doc/Makefile | 2 pomp-0.18-3/pomp/inst/doc/compiled_code_in_pomp.Rnw |only pomp-0.18-3/pomp/inst/doc/compiled_code_in_pomp.pdf |only pomp-0.18-3/pomp/inst/doc/random_walk.Rnw | 196 +++------------- pomp-0.18-3/pomp/inst/doc/random_walk.pdf |binary pomp-0.18-3/pomp/inst/examples/sir.R | 81 ++++-- pomp-0.18-3/pomp/inst/examples/sir.c | 133 +++++++++-- pomp-0.18-3/pomp/inst/include/euler.h | 18 + pomp-0.18-3/pomp/inst/include/lookup_table.h |only pomp-0.18-3/pomp/man/euler.Rd | 173 +++++++++++++- pomp-0.18-3/pomp/man/eulermultinom.Rd | 2 pomp-0.18-3/pomp/man/mif-methods.Rd | 6 pomp-0.18-3/pomp/man/mif.Rd | 2 pomp-0.18-3/pomp/man/pfilter.Rd | 2 pomp-0.18-3/pomp/man/pomp-class.Rd | 15 - pomp-0.18-3/pomp/man/pomp-package.Rd | 6 pomp-0.18-3/pomp/man/pomp.Rd | 13 - pomp-0.18-3/pomp/src/euler.c | 234 +++++++++++--------- pomp-0.18-3/pomp/src/euler.h | 19 + pomp-0.18-3/pomp/src/eulermultinom.c | 71 ++++-- pomp-0.18-3/pomp/src/lookup_table.c |only pomp-0.18-3/pomp/src/lookup_table.h |only pomp-0.18-3/pomp/src/ou2.c | 77 +----- pomp-0.18-3/pomp/src/pomp.h | 48 ++++ pomp-0.18-3/pomp/src/resample.c | 12 - pomp-0.18-3/pomp/src/sir.c |only pomp-0.18-3/pomp/tests/ou2-simulate.R | 4 50 files changed, 1037 insertions(+), 768 deletions(-)
Author: Ben B. Hansen
Diff between optmatch versions 0.3-8 dated 2008-05-13 and 0.3-9 dated 2008-05-14
Title: Functions for optimal matching
Description: Functions to perform optimal matching, particularly full matching
ChangeLog | 2 ++
DESCRIPTION | 6 +++---
R/mahal.dist.R | 7 +++++--
inst/doc/optmatch.pdf |binary
tests/mahal-dist.R | 2 ++
tests/mahal-dist.Rout.save | 9 +++++++--
6 files changed, 19 insertions(+), 7 deletions(-)
Author: Grant Izmirlian
Title: Power in a Group Sequential Design
Description: Tools to compute power in a group sequential design. SimPwrGSD C-kernel is a simulation routine that is similar in spirit to dssp2.f by Gu and Lai, but with major improvements. AsyPwrGSD has exactly the same range of application as SimPwrGSD but uses asymptotic methods and runs _much_ faster.
Diff between PwrGSD versions 1.0 dated 2008-01-07 and 1.1 dated 2008-05-14
PwrGSD-1.0/PwrGSD/inst/doc/PwrGSD.pdf |only PwrGSD-1.0/PwrGSD/inst/doc/notes.tex |only PwrGSD-1.1/PwrGSD/DESCRIPTION | 6 +++--- PwrGSD-1.1/PwrGSD/INDEX | 4 +++- PwrGSD-1.1/PwrGSD/R/PwrGSD.R | 2 +- PwrGSD-1.1/PwrGSD/inst/doc/Ch6-GrpSeqBnds.Rd |only PwrGSD-1.1/PwrGSD/inst/doc/GrpSeqBnds-vignette-1-fig1-LanDemets.eps |only PwrGSD-1.1/PwrGSD/inst/doc/GrpSeqBnds-vignette-1-fig1-LanDemets.pdf |only PwrGSD-1.1/PwrGSD/inst/doc/GrpSeqBnds-vignette-1-fig2-StochCurt.eps |only PwrGSD-1.1/PwrGSD/inst/doc/GrpSeqBnds-vignette-1-fig2-StochCurt.pdf |only PwrGSD-1.1/PwrGSD/inst/doc/GrpSeqBnds-vignette-1.Rnw |only PwrGSD-1.1/PwrGSD/inst/doc/GrpSeqBnds-vignette-1.aux |only PwrGSD-1.1/PwrGSD/inst/doc/GrpSeqBnds-vignette-1.dvi |only PwrGSD-1.1/PwrGSD/inst/doc/GrpSeqBnds-vignette-1.log |only PwrGSD-1.1/PwrGSD/inst/doc/GrpSeqBnds-vignette-1.out |only PwrGSD-1.1/PwrGSD/inst/doc/GrpSeqBnds-vignette-1.pdf |only PwrGSD-1.1/PwrGSD/inst/doc/GrpSeqBnds-vignette-1.tex |only PwrGSD-1.1/PwrGSD/inst/doc/PwrGSD-manual.pdf |binary PwrGSD-1.1/PwrGSD/inst/doc/PwrGSD-vignette-1.Rnw |only PwrGSD-1.1/PwrGSD/inst/doc/PwrGSD-vignette-1.pdf |only PwrGSD-1.1/PwrGSD/inst/doc/Rplots.ps |only PwrGSD-1.1/PwrGSD/inst/doc/clearance.jpg |only PwrGSD-1.1/PwrGSD/inst/doc/cpd-PwrGSD-vignette-1-fig1-LanDemets.eps |only PwrGSD-1.1/PwrGSD/inst/doc/cpd-PwrGSD-vignette-1-fig1-LanDemets.pdf |only PwrGSD-1.1/PwrGSD/inst/doc/cpd-PwrGSD-vignette-1-fig2-StochCurt.eps |only PwrGSD-1.1/PwrGSD/inst/doc/cpd-PwrGSD-vignette-1-fig2-StochCurt.pdf |only PwrGSD-1.1/PwrGSD/inst/doc/cpd-PwrGSD-vignette-1.Rnw |only PwrGSD-1.1/PwrGSD/inst/doc/cpd-PwrGSD-vignette-1.aux |only PwrGSD-1.1/PwrGSD/inst/doc/cpd-PwrGSD-vignette-1.log |only PwrGSD-1.1/PwrGSD/inst/doc/cpd-PwrGSD-vignette-1.out |only PwrGSD-1.1/PwrGSD/inst/doc/cpd-PwrGSD-vignette-1.pdf |only PwrGSD-1.1/PwrGSD/inst/doc/cpd-PwrGSD-vignette-1.tex |only PwrGSD-1.1/PwrGSD/man/Ch2-cpd.PwrGSD.Rd | 3 +-- 33 files changed, 8 insertions(+), 7 deletions(-)
Author: Original by Joseph L. Schafer
Diff between pan versions 0.2-4 dated 2007-10-02 and 0.2-6 dated 2008-05-14
Title: Multiple imputation for multivariate panel or clustered data
Description: Multiple imputation for multivariate panel or clustered data
DESCRIPTION | 11 ++++-------
LICENSE |only
R/pan.R | 2 +-
3 files changed, 5 insertions(+), 8 deletions(-)
Author: Thomas W. Yee
Diff between VGAM versions 0.7-6 dated 2008-03-21 and 0.7-7 dated 2008-05-14
Title: Vector Generalized Linear and Additive Models
Description: Vector generalized linear and additive models, and
associated models (Reduced-Rank VGLMs, Quadratic RR-VGLMs,
Reduced-Rank VGAMs). This package fits many models and
distribution by maximum likelihood estimation (MLE) or
penalized MLE. Also fits constrained ordination models in
ecology.
DESCRIPTION | 6
NAMESPACE | 6
NEWS | 27 ++
R/aamethods.q | 4
R/cao.fit.q | 17 -
R/coef.vlm.q | 2
R/cqo.fit.q | 12 -
R/family.binomial.q | 452 ++++++++++++++++++++++++++++++++++++++----------
R/family.categorical.q | 6
R/family.extremes.q | 4
R/family.functions.q | 8
R/family.genetic.q | 2
R/family.glmgam.q | 2
R/family.normal.q | 4
R/family.qreg.q | 7
R/family.rcqo.q | 129 ++++++++-----
R/family.rrr.q | 155 +++++++++++-----
R/family.univariate.q | 25 +-
R/family.zeroinf.q | 26 +-
R/model.matrix.vglm.q | 2
R/mux.q | 18 +
R/plot.vglm.q | 2
R/predict.vgam.q | 4
R/residuals.vlm.q | 6
R/rrvglm.fit.q | 18 -
R/summary.vglm.q | 2
R/vgam.R | 2
R/vgam.fit.q | 19 --
R/vglm.fit.q | 29 +--
R/vlm.wfit.q | 2
man/acat.Rd | 2
man/alaplace3.Rd | 47 ++++
man/alsqreg.Rd | 13 -
man/amlbinomial.Rd | 5
man/amlexponential.Rd | 5
man/amlpoisson.Rd | 5
man/binom2.or.Rd | 51 +++--
man/binom2.orUC.Rd |only
man/cqo.Rd | 4
man/fisherz.Rd | 13 -
man/gamma1.Rd | 3
man/lgammaff.Rd | 1
man/lms.bcn.Rd | 1
man/mbinomial.Rd | 5
man/notdocumentedyet.Rd | 2
man/predict.qrrvglm.Rd |only
man/rcqo.Rd | 20 +-
man/zinbUC.Rd | 8
man/zipebcom.Rd |only
man/zipoisson.Rd | 17 +
src/testf90.f90 | 66 +++++--
51 files changed, 905 insertions(+), 361 deletions(-)