Title: Useful tools for structural equation modeling.
Diff between semTools versions 0.2-7 dated 2012-10-16 and 0.2-8 dated 2012-10-26
Description: This package provide useful tools for structural equation
modeling analysis.
Author: Sunthud Pornprasertmanit
Maintainer: Sunthud Pornprasertmanit
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/runMI.R | 49 +++++++++++++++++++++++++++++++++++++++++++++++--
man/runMI.Rd | 1 +
4 files changed, 55 insertions(+), 9 deletions(-)
Title: Joint modelling of repeated measurements and time-to-event data
Diff between joineR versions 1.0-2 dated 2012-06-05 and 1.0-3 dated 2012-10-26
Description: Analysis of repeated measurements and time-to-event data
via random effects joint models. Some plotting functions and
the variogram are also included.
Author: Pete Philipson, Ines Sousa, Peter Diggle, Paula Williamson,
Ruwanthi Kolamunnage-Dona, Robin Henderson
Maintainer: Pete Philipson
DESCRIPTION | 11 +--
MD5 | 30 ++++----
NAMESPACE | 3
R/joint.R | 183 +++++++++++++++++++++++++++++---------------------
R/jointSE.R | 19 ++---
R/sample.jointdata.R | 89 ++++++++++++------------
R/summary.joint.R | 7 +
R/summary.jointdata.R | 14 +--
R/summarybal.R |only
inst/doc/joineR.Rnw | 10 ++
inst/doc/joineR.pdf |binary
man/joint.Rd | 10 +-
man/jointSE.Rd | 2
man/plot.vargm.Rd | 8 +-
man/summarybal.Rd |only
man/variogram.Rd | 6 -
vignettes/joineR.Rnw | 10 ++
17 files changed, 231 insertions(+), 171 deletions(-)
Title: Regression Discontinuity Estimation
Diff between rdd versions 0.42 dated 2012-09-08 and 0.50 dated 2012-10-26
Description: This package provides the tools to undertake estimation in
Regression Discontinuity Designs. Both sharp and fuzzy designs
are supported. Estimation is accomplished using local linear
regression. A provided function will utilize
Imbens-Kalyanaraman optimal bandwidth calculation. A function
is also included to test the assumption of no-sorting effects.
Author: Drew Dimmery
Maintainer: Drew Dimmery
DESCRIPTION | 4 +-
MD5 | 10 +++----
R/DCdensity.R | 78 ++++++++++++++++++++++++--------------------------------
R/IKbandwidth.R | 10 ++++++-
R/plot.RD.R | 2 -
VERSION | 5 +++
6 files changed, 56 insertions(+), 53 deletions(-)
Title: A package to estimate posterior probabilities and perform model
selection in change-point models using constrained HMM.
Diff between postCP versions 1.6.0 dated 2012-10-23 and 1.6.1 dated 2012-10-26
Description: The functions are used for change-point problems, after an
initial set of change-points within the data has already been
obtained. The function postCP obtains estimates of posterior
probabilities of change-point and hidden states for each
observation, and confidence intervals for the positions of the
change-point. The function postCPsample obtains random samples
of sets of change-points using the output of the postCP
function. Model selection may be performed using function
postCPmodelsel through criteria obtained from function
postCPcrit.
Author: Gregory Nuel and The Minh Luong
Maintainer: The Minh Luong
DESCRIPTION | 6 +++---
MD5 | 23 ++++++++++++-----------
man/GreedySegmente.Rd | 2 +-
man/lesum.Rd | 2 +-
man/mleNB.Rd | 2 +-
man/plot.postCP.Rd | 2 +-
man/postCP.Rd | 2 +-
man/postCPcrit.Rd | 2 +-
man/postCPmodelsel.Rd | 2 +-
man/postCPsample.Rd | 2 +-
man/viterbi.Rd | 2 +-
src/Makevars |only
src/postCP.cpp | 33 ++++++++-------------------------
13 files changed, 32 insertions(+), 48 deletions(-)
Title: Diversity-dependent diversification
Diff between DDD versions 1.5 dated 2012-10-02 and 1.7 dated 2012-10-26
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. 180: E75-E89, doi: 10.1086/667574.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne
DDD-1.5/DDD/R/optimx2.R |only
DDD-1.7/DDD/DESCRIPTION | 13 ++++----
DDD-1.7/DDD/MD5 | 34 ++++++++++++----------
DDD-1.7/DDD/R/dd_KI_ML.R | 58 ++++++++++++++++++++++++++++++--------
DDD-1.7/DDD/R/dd_KI_loglik.R | 16 +++++++---
DDD-1.7/DDD/R/dd_KI_simplex.R |only
DDD-1.7/DDD/R/dd_ML.R | 57 ++++++++++++++++++++++++++++++--------
DDD-1.7/DDD/R/dd_SR_ML.R | 60 ++++++++++++++++++++++++++++++----------
DDD-1.7/DDD/R/dd_SR_loglik.R | 15 +++++++---
DDD-1.7/DDD/R/dd_SR_simplex.R |only
DDD-1.7/DDD/R/dd_loglik.R | 19 ++++++++----
DDD-1.7/DDD/R/dd_simplex.R |only
DDD-1.7/DDD/man/DDD-internal.Rd | 4 ++
DDD-1.7/DDD/man/DDD-package.Rd | 10 +++++-
DDD-1.7/DDD/man/dd_KI_ML.Rd | 14 ++++++---
DDD-1.7/DDD/man/dd_KI_loglik.Rd | 5 ++-
DDD-1.7/DDD/man/dd_ML.Rd | 30 ++++++++++++--------
DDD-1.7/DDD/man/dd_SR_ML.Rd | 17 ++++++++---
DDD-1.7/DDD/man/dd_SR_loglik.Rd | 5 ++-
DDD-1.7/DDD/man/dd_loglik.Rd | 5 ++-
20 files changed, 258 insertions(+), 104 deletions(-)
Title: Data Modelling with Additive Bayesian Networks
Diff between abn versions 0.7 dated 2012-04-19 and 0.8 dated 2012-10-26
Description: Additive Bayesian network models are equivalent to
multivariate regression using graphical modelling. This library
provides routines to help determine optimal Bayesian network
models for a given data set, where these models are used to
identify statistical dependencies in messy, complex data. The
additive formulation of these models is equivalent to
multivariate generalised linear modelling (including mixed
models). The usual term to describe this model selection
process is structure discovery. The core functionality is
concerned with model selection - determining the most robust
empirical model of data from interdependent variables. A
comprehensive set of documented case studies, numerical
accuracy/quality assurance exercises, and additional
documentation are available from the abn website.
Author: Fraser Lewis
Maintainer: Fraser Lewis
abn-0.7/abn/R/allnodesabn.r |only
abn-0.7/abn/R/allnodesbn.r |only
abn-0.7/abn/R/arcfreq.r |only
abn-0.7/abn/R/bn-internal.r |only
abn-0.7/abn/R/findmostprobablebn.r |only
abn-0.7/abn/R/fitabn.r |only
abn-0.7/abn/R/fitbn.r |only
abn-0.7/abn/R/getmarginal.r |only
abn-0.7/abn/R/getposteriorfeaturesbn.r |only
abn-0.7/abn/R/hillsearchabn.r |only
abn-0.7/abn/R/hillsearchbn.r |only
abn-0.7/abn/R/searchabn.r |only
abn-0.7/abn/R/searchbn.r |only
abn-0.7/abn/R/tographviz.r |only
abn-0.7/abn/R/unique_nets.r |only
abn-0.7/abn/cleanup |only
abn-0.7/abn/data/pigs1par.RData |only
abn-0.7/abn/data/var33.RData |only
abn-0.7/abn/inst |only
abn-0.7/abn/man/allnodesabn.Rd |only
abn-0.7/abn/man/allnodesbn.Rd |only
abn-0.7/abn/man/arcfreq.Rd |only
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abn-0.7/abn/man/findmostprobablebn.Rd |only
abn-0.7/abn/man/fitbn.Rd |only
abn-0.7/abn/man/getmarginal.Rd |only
abn-0.7/abn/man/getposteriorfeaturesbn.Rd |only
abn-0.7/abn/man/hillsearchabn.Rd |only
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abn-0.7/abn/man/unique.nets.Rd |only
abn-0.7/abn/man/var33.rd |only
abn-0.7/abn/src/Makevars |only
abn-0.7/abn/src/README.profiling |only
abn-0.7/abn/src/allnodesbn.c |only
abn-0.7/abn/src/allnodesbn_additive.c |only
abn-0.7/abn/src/fitnetwork.c |only
abn-0.7/abn/src/fitnetwork_additive.c |only
abn-0.7/abn/src/fitnetwork_multi.c |only
abn-0.7/abn/src/getmarginals_additive.c |only
abn-0.7/abn/src/getposterior_features.c |only
abn-0.7/abn/src/getposterior_features_max.c |only
abn-0.7/abn/src/hillsearchfornetwork.c |only
abn-0.7/abn/src/hillsearchfornetwork_additive.c |only
abn-0.7/abn/src/laplace.c |only
abn-0.7/abn/src/laplace.h |only
abn-0.7/abn/src/laplace_marginals.c |only
abn-0.7/abn/src/laplace_marginals.h |only
abn-0.7/abn/src/makefile.customunix |only
abn-0.7/abn/src/makefile.customwin |only
abn-0.7/abn/src/network.c |only
abn-0.7/abn/src/network.h |only
abn-0.7/abn/src/network_laplace.c |only
abn-0.7/abn/src/network_laplace.h |only
abn-0.7/abn/src/scorereuse.c |only
abn-0.7/abn/src/scorereuse.h |only
abn-0.7/abn/src/searchfornetwork.c |only
abn-0.7/abn/src/searchfornetwork_additive.c |only
abn-0.7/abn/src/searchfornetwork_additive.h |only
abn-0.7/abn/src/utility_fns.c |only
abn-0.7/abn/src/utility_fns.h |only
abn-0.7/abn/vignettes |only
abn-0.8/abn/DESCRIPTION | 43 -
abn-0.8/abn/MD5 | 176 ++---
abn-0.8/abn/NAMESPACE | 29
abn-0.8/abn/R/abn-internal.R |only
abn-0.8/abn/R/buildscorecache.R |only
abn-0.8/abn/R/buildscorecache_inla.R |only
abn-0.8/abn/R/calc_node_mlik_inla.R |only
abn-0.8/abn/R/calc_node_mlik_inla_mixed.R |only
abn-0.8/abn/R/fitabn.R |only
abn-0.8/abn/R/fitabn_inla.R |only
abn-0.8/abn/R/mostprobable.R |only
abn-0.8/abn/R/search_hillclimber.R |only
abn-0.8/abn/R/tographviz.R |only
abn-0.8/abn/TODO |only
abn-0.8/abn/configure | 2
abn-0.8/abn/configure.ac | 2
abn-0.8/abn/data/ex0data.RData |only
abn-0.8/abn/data/ex1data.RData |only
abn-0.8/abn/data/ex2data.RData |only
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abn-0.8/abn/man/build_score_cache.Rd |only
abn-0.8/abn/man/build_score_cache_inla.Rd |only
abn-0.8/abn/man/calc_node_mlike_inla.Rd |only
abn-0.8/abn/man/calc_node_mlike_inla_mixed.Rd |only
abn-0.8/abn/man/dag_ex0.Rd |only
abn-0.8/abn/man/dag_ex1.Rd |only
abn-0.8/abn/man/dag_ex2.Rd |only
abn-0.8/abn/man/dag_ex3.Rd |only
abn-0.8/abn/man/dag_ex4.Rd |only
abn-0.8/abn/man/dag_ex5.Rd |only
abn-0.8/abn/man/fitabn.Rd | 359 ++++++++----
abn-0.8/abn/man/fitabn_inla.Rd |only
abn-0.8/abn/man/mostprobable.Rd |only
abn-0.8/abn/man/search_hillclimber.Rd |only
abn-0.8/abn/man/tographviz.Rd | 152 +++--
abn-0.8/abn/src/Makevars.in | 8
abn-0.8/abn/src/Makevars.win | 28
abn-0.8/abn/src/buildcachematrix.c |only
abn-0.8/abn/src/buildcachematrix.h |only
abn-0.8/abn/src/cycles.c |only
abn-0.8/abn/src/cycles.h |only
abn-0.8/abn/src/fitabn.c |only
abn-0.8/abn/src/fitabn_marginals.c |only
abn-0.8/abn/src/fitnodes.c |only
abn-0.8/abn/src/fitnodes.h |only
abn-0.8/abn/src/makefile.custom |only
abn-0.8/abn/src/mobius.c | 619 ++++-----------------
abn-0.8/abn/src/mobius.h | 32 -
abn-0.8/abn/src/mostprobable.c |only
abn-0.8/abn/src/network_score.c |only
abn-0.8/abn/src/network_score.h |only
abn-0.8/abn/src/node_binomial.c |only
abn-0.8/abn/src/node_binomial.h |only
abn-0.8/abn/src/node_binomial_marginals_rv_Rsupp.c |only
abn-0.8/abn/src/node_binomial_marginals_rv_Rsupp.h |only
abn-0.8/abn/src/node_binomial_rv_Rsupp.c |only
abn-0.8/abn/src/node_binomial_rv_Rsupp.h |only
abn-0.8/abn/src/node_binomial_rv_inner.c |only
abn-0.8/abn/src/node_binomial_rv_inner.h |only
abn-0.8/abn/src/node_gaussian.c |only
abn-0.8/abn/src/node_gaussian.h |only
abn-0.8/abn/src/node_poisson.c |only
abn-0.8/abn/src/node_poisson.h |only
abn-0.8/abn/src/searchhill.c |only
abn-0.8/abn/src/searchhill.h |only
abn-0.8/abn/src/structs.h | 123 ++--
abn-0.8/abn/src/utility.c |only
abn-0.8/abn/src/utility.h |only
135 files changed, 682 insertions(+), 891 deletions(-)
Title: Recursive Partitioning
Diff between rpart versions 3.1-55 dated 2012-10-07 and 4.0-1 dated 2012-10-26
Description: Recursive partitioning and regression trees
Author: Terry Therneau [aut], Beth Atkinson [aut], Brian Ripley [aut,
trl, cre] (author of R port)
Maintainer: Brian Ripley
rpart-3.1-55/rpart/INDEX |only
rpart-3.1-55/rpart/Readme |only
rpart-3.1-55/rpart/data/car.test.frame.csv |only
rpart-3.1-55/rpart/data/kyphosis.tab |only
rpart-3.1-55/rpart/data/solder.tab |only
rpart-3.1-55/rpart/src/rpartS.h |only
rpart-3.1-55/rpart/src/s_to_rp.c |only
rpart-3.1-55/rpart/tests/rpartco.R |only
rpart-3.1-55/rpart/tests/surv_test.R |only
rpart-4.0-1/rpart/ChangeLog | 8
rpart-4.0-1/rpart/Changelog.TMT |only
rpart-4.0-1/rpart/DESCRIPTION | 14
rpart-4.0-1/rpart/MD5 | 229 +--
rpart-4.0-1/rpart/NAMESPACE | 1
rpart-4.0-1/rpart/R/labels.rpart.R | 4
rpart-4.0-1/rpart/R/plot.rpart.R | 23
rpart-4.0-1/rpart/R/plotcp.R | 2
rpart-4.0-1/rpart/R/post.rpart.R | 2
rpart-4.0-1/rpart/R/pred.rpart.R | 40
rpart-4.0-1/rpart/R/predict.rpart.R | 15
rpart-4.0-1/rpart/R/printcp.R | 1
rpart-4.0-1/rpart/R/prune.R | 1
rpart-4.0-1/rpart/R/roc.rpart.R |only
rpart-4.0-1/rpart/R/rpart.R | 364 ++--
rpart-4.0-1/rpart/R/rpart.anova.R | 2
rpart-4.0-1/rpart/R/rpart.branch.R | 9
rpart-4.0-1/rpart/R/rpart.class.R | 33
rpart-4.0-1/rpart/R/rpart.control.R | 2
rpart-4.0-1/rpart/R/rpart.exp.R | 6
rpart-4.0-1/rpart/R/rpart.matrix.R | 2
rpart-4.0-1/rpart/R/rpart.poisson.R | 7
rpart-4.0-1/rpart/R/rpartco.R | 51
rpart-4.0-1/rpart/R/rpartpl.R |only
rpart-4.0-1/rpart/R/rpconvert.R | 2
rpart-4.0-1/rpart/R/snip.rpart.R | 1
rpart-4.0-1/rpart/R/snip.rpart.mouse.R | 19
rpart-4.0-1/rpart/R/summary.rpart.R | 4
rpart-4.0-1/rpart/R/text.rpart.R | 17
rpart-4.0-1/rpart/R/xpred.rpart.R | 108 -
rpart-4.0-1/rpart/R/zzz.R | 2
rpart-4.0-1/rpart/data/car.test.frame.csv.gz |only
rpart-4.0-1/rpart/data/kyphosis.tab.gz |only
rpart-4.0-1/rpart/data/solder.tab.gz |only
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rpart-4.0-1/rpart/inst/po/de/LC_MESSAGES/R-rpart.mo |binary
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rpart-4.0-1/rpart/inst/po/en@quot/LC_MESSAGES/R-rpart.mo |binary
rpart-4.0-1/rpart/inst/po/en@quot/LC_MESSAGES/rpart.mo |binary
rpart-4.0-1/rpart/inst/po/fr/LC_MESSAGES/R-rpart.mo |binary
rpart-4.0-1/rpart/inst/po/fr/LC_MESSAGES/rpart.mo |binary
rpart-4.0-1/rpart/inst/po/pl/LC_MESSAGES/R-rpart.mo |binary
rpart-4.0-1/rpart/inst/po/pl/LC_MESSAGES/rpart.mo |binary
rpart-4.0-1/rpart/inst/po/ru/LC_MESSAGES/R-rpart.mo |binary
rpart-4.0-1/rpart/inst/po/ru/LC_MESSAGES/rpart.mo |binary
rpart-4.0-1/rpart/man/path.rpart.Rd | 2
rpart-4.0-1/rpart/man/plot.rpart.Rd | 5
rpart-4.0-1/rpart/man/post.rpart.Rd | 2
rpart-4.0-1/rpart/man/predict.rpart.Rd | 2
rpart-4.0-1/rpart/man/rpart-internal.Rd | 8
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rpart-4.0-1/rpart/man/stagec.Rd |only
rpart-4.0-1/rpart/man/text.rpart.Rd | 2
rpart-4.0-1/rpart/man/xpred.rpart.Rd | 15
rpart-4.0-1/rpart/po/R-de.po | 142 -
rpart-4.0-1/rpart/po/R-fr.po | 14
rpart-4.0-1/rpart/po/R-pl.po | 388 ++---
rpart-4.0-1/rpart/po/R-rpart.pot | 16
rpart-4.0-1/rpart/po/R-ru.po | 14
rpart-4.0-1/rpart/po/de.po | 59
rpart-4.0-1/rpart/po/fr.po | 29
rpart-4.0-1/rpart/po/pl.po | 29
rpart-4.0-1/rpart/po/rpart.pot | 30
rpart-4.0-1/rpart/po/ru.po | 29
rpart-4.0-1/rpart/src/anova.c | 78 -
rpart-4.0-1/rpart/src/anovapred.c | 4
rpart-4.0-1/rpart/src/branch.c | 70
rpart-4.0-1/rpart/src/bsplit.c | 41
rpart-4.0-1/rpart/src/choose_surg.c | 132 -
rpart-4.0-1/rpart/src/fix_cp.c | 4
rpart-4.0-1/rpart/src/free_tree.c | 33
rpart-4.0-1/rpart/src/func_table.h | 39
rpart-4.0-1/rpart/src/gini.c | 96 -
rpart-4.0-1/rpart/src/graycode.c | 40
rpart-4.0-1/rpart/src/init.c | 26
rpart-4.0-1/rpart/src/insert_split.c | 33
rpart-4.0-1/rpart/src/make_cp_list.c | 21
rpart-4.0-1/rpart/src/make_cp_table.c | 9
rpart-4.0-1/rpart/src/mysort.c | 182 +-
rpart-4.0-1/rpart/src/node.h | 19
rpart-4.0-1/rpart/src/nodesplit.c | 236 ++-
rpart-4.0-1/rpart/src/partition.c | 79 -
rpart-4.0-1/rpart/src/poisson.c | 84 -
rpart-4.0-1/rpart/src/pred_rpart.c | 108 -
rpart-4.0-1/rpart/src/rpart.c | 352 +++-
rpart-4.0-1/rpart/src/rpart.h | 31
rpart-4.0-1/rpart/src/rpart_callback.c | 15
rpart-4.0-1/rpart/src/rpartexp.c |only
rpart-4.0-1/rpart/src/rpartexp2.c | 23
rpart-4.0-1/rpart/src/rpartproto.h | 92 -
rpart-4.0-1/rpart/src/rpcountup.c | 34
rpart-4.0-1/rpart/src/rpmatrix.c | 59
rpart-4.0-1/rpart/src/rundown.c | 25
rpart-4.0-1/rpart/src/rundown2.c | 28
rpart-4.0-1/rpart/src/s_xpred.c | 155 +-
rpart-4.0-1/rpart/src/surrogate.c | 70
rpart-4.0-1/rpart/src/usersplit.c | 60
rpart-4.0-1/rpart/src/xpred.c |only
rpart-4.0-1/rpart/src/xval.c | 136 +
rpart-4.0-1/rpart/tests/Examples/rpart-Ex.Rout.save | 313 +---
rpart-4.0-1/rpart/tests/backticks.Rout.save |only
rpart-4.0-1/rpart/tests/cost.R |only
rpart-4.0-1/rpart/tests/cost.Rout.save |only
rpart-4.0-1/rpart/tests/cptest.R |only
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rpart-4.0-1/rpart/tests/priors.R |only
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rpart-4.0-1/rpart/tests/rescale.R |only
rpart-4.0-1/rpart/tests/rescale.Rout.save |only
rpart-4.0-1/rpart/tests/testall.R | 278 ---
rpart-4.0-1/rpart/tests/testall.Rout.save | 1098 +++------------
rpart-4.0-1/rpart/tests/treble.R |only
rpart-4.0-1/rpart/tests/treble.Rout.save |only
rpart-4.0-1/rpart/tests/treble2.R |only
rpart-4.0-1/rpart/tests/treble2.Rout.save |only
rpart-4.0-1/rpart/tests/treble3.R |only
rpart-4.0-1/rpart/tests/treble3.Rout.save |only
rpart-4.0-1/rpart/tests/treble4.R |only
rpart-4.0-1/rpart/tests/treble4.Rout.save |only
rpart-4.0-1/rpart/tests/usersplits.R | 24
rpart-4.0-1/rpart/tests/usersplits.Rout.save | 32
rpart-4.0-1/rpart/tests/xpred1.R |only
rpart-4.0-1/rpart/tests/xpred1.Rout.save |only
rpart-4.0-1/rpart/tests/xpred2.R |only
rpart-4.0-1/rpart/tests/xpred2.Rout.save |only
rpart-4.0-1/rpart/vignettes |only
137 files changed, 2737 insertions(+), 3177 deletions(-)
Title: Power and Sample size based on two one-sided t-tests (TOST) for
(bio)equivalence studies
Diff between PowerTOST versions 0.9-11 dated 2012-08-07 and 1.0-00 dated 2012-10-26
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies. See
function known.designs() for study designs covered. Moreover
the package contains functions for power and sample size based
on 'expected' power in case of uncertain (estimated)
variability. ----- Added are functions for the power and
sample size for the ratio of two means with normally
distributed data on the original scale (based on Fieller's
confidence ('fiducial') interval). ----- Contains further
functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but
eventually useful if the question of 'non-superiority' must be
evaluated. The power and sample size calculations based on
non-inferiority test may also performed via 'expected' power in
case of uncertain (estimated) variability.
Author: Detlew Labes
Maintainer: D. Labes
DESCRIPTION | 10 +++++-----
MD5 | 34 ++++++++++++++++++----------------
NAMESPACE | 6 ++++--
NEWS | 7 +++++++
R/DesignHelpers.R | 11 ++++++++++-
R/SampleSize.R | 8 ++------
R/SampleSize_noninf.R | 10 +++-------
R/expSampleSize.R | 10 +++-------
R/expSampleSize_noninf.R | 10 +++-------
R/exppower.R | 7 +------
R/exppower_noninf.R | 7 +------
R/helper.R |only
R/power.R | 17 +++++------------
R/power2.R | 18 ++++++++----------
R/power_noninf.R | 16 ++++++++--------
man/CV2se.Rd | 21 +++++++++++++++------
man/CVCL.Rd |only
man/OwensT.Rd | 3 ++-
man/PowerTOST-package.Rd | 4 ++--
19 files changed, 97 insertions(+), 102 deletions(-)
Title: Tools to analyse RFLP data
Diff between RFLPtools versions 1.3 dated 2010-07-24 and 1.4 dated 2012-10-26
Description: RFLPtools provides functions to analyse DNA fragment
samples (i.e. derived from RFLP-analysis) and standalone BLAST
report files (i.e. DNA sequence analysis).
Author: Fabienne Flessa, Alexandra Kehl, Matthias Kohl
Maintainer: Matthias Kohl
RFLPtools-1.3/RFLPtools/inst/doc/PaulMartini.png |only
RFLPtools-1.3/RFLPtools/inst/doc/logoUBT.png |only
RFLPtools-1.4/RFLPtools/DESCRIPTION | 8 -
RFLPtools-1.4/RFLPtools/MD5 |only
RFLPtools-1.4/RFLPtools/NAMESPACE | 1
RFLPtools-1.4/RFLPtools/NEWS | 36 +++--
RFLPtools-1.4/RFLPtools/R/RFLPdist.R | 3
RFLPtools-1.4/RFLPtools/R/RFLPdist2.R | 4
RFLPtools-1.4/RFLPtools/R/RFLPdist2ref.R | 2
RFLPtools-1.4/RFLPtools/R/RFLPplot.R | 3
RFLPtools-1.4/RFLPtools/R/diffDist.R | 6
RFLPtools-1.4/RFLPtools/R/linCombDist.R |only
RFLPtools-1.4/RFLPtools/R/read.blast.R | 9 -
RFLPtools-1.4/RFLPtools/inst/doc/RFLPtools.Rnw | 76 ++++++++---
RFLPtools-1.4/RFLPtools/inst/doc/RFLPtools.pdf |binary
RFLPtools-1.4/RFLPtools/man/0RFLP-package.Rd | 146 +++++++++++------------
RFLPtools-1.4/RFLPtools/man/RFLPdist.Rd | 2
RFLPtools-1.4/RFLPtools/man/RFLPdist2.Rd | 2
RFLPtools-1.4/RFLPtools/man/RFLPdist2ref.Rd | 2
RFLPtools-1.4/RFLPtools/man/RFLPplot.Rd | 2
RFLPtools-1.4/RFLPtools/man/RFLPqc.Rd | 2
RFLPtools-1.4/RFLPtools/man/RFLPrefplot.Rd | 2
RFLPtools-1.4/RFLPtools/man/linCombDist.Rd |only
RFLPtools-1.4/RFLPtools/man/nrBands.Rd | 2
RFLPtools-1.4/RFLPtools/man/read.blast.Rd | 27 +++-
RFLPtools-1.4/RFLPtools/man/read.rflp.Rd | 2
RFLPtools-1.4/RFLPtools/man/sim2dist.Rd | 2
RFLPtools-1.4/RFLPtools/man/simMatrix.Rd | 2
RFLPtools-1.4/RFLPtools/man/write.hclust.Rd | 2
RFLPtools-1.4/RFLPtools/vignettes |only
30 files changed, 206 insertions(+), 137 deletions(-)
Title: Tools for analysing OmniLog(R) Phenotype Microarray data
Diff between opm versions 0.6-0 dated 2012-08-23 and 0.7-0 dated 2012-10-26
Description: Tools for analysing OmniLog(R) Phenotype Microarray (PM)
data as produced by the device distributed by BiOLOG Inc.,
including plotting, aggregating (estimating curve parameters),
comparing and discretizing PM data, creating phylogenetic
formats and reports for taxonomic journals, integrating
metadata, using the YAML format for the storage of data and
metadata, and batch conversion of large numbers of files.
Author: Markus Goeker, with contributions by Lea A.I. Vaas, Johannes
Sikorski, Nora Buddruhs and Anne Fiebig
Maintainer: Markus Goeker
opm-0.6-0/opm/data/datalist |only
opm-0.6-0/opm/data/vaas_et_al.rda |only
opm-0.6-0/opm/man/L.Rd |only
opm-0.6-0/opm/man/LL.Rd |only
opm-0.6-0/opm/man/assert_class.Rd |only
opm-0.6-0/opm/man/case.Rd |only
opm-0.6-0/opm/man/extract_curve_params.grofit.Rd |only
opm-0.6-0/opm/man/group_by_sep.Rd |only
opm-0.6-0/opm/man/listing.Rd |only
opm-0.6-0/opm/man/max_rgb_contrast.Rd |only
opm-0.6-0/opm/man/must.Rd |only
opm-0.6-0/opm/man/mypdf.Rd |only
opm-0.6-0/opm/man/paper_size.Rd |only
opm-0.6-0/opm/man/run_native_kmeans.Rd |only
opm-0.6-0/opm/man/taste.Rd |only
opm-0.6-0/opm/man/vaas_et_al.Rd |only
opm-0.7-0/opm/ChangeLog | 29 +
opm-0.7-0/opm/DESCRIPTION | 18
opm-0.7-0/opm/MD5 | 243 ++++----
opm-0.7-0/opm/NAMESPACE | 15
opm-0.7-0/opm/NEWS | 35 +
opm-0.7-0/opm/R/aggregation.R | 16
opm-0.7-0/opm/R/auxiliary.R | 659 +++++++----------------
opm-0.7-0/opm/R/classes.R | 123 +++-
opm-0.7-0/opm/R/combination.R | 8
opm-0.7-0/opm/R/constants.R | 40 -
opm-0.7-0/opm/R/conversion.R | 163 ++++-
opm-0.7-0/opm/R/data.R | 48 -
opm-0.7-0/opm/R/discretization.R |only
opm-0.7-0/opm/R/getter.R | 304 ++++++++--
opm-0.7-0/opm/R/io.R | 45 -
opm-0.7-0/opm/R/kmeans.R | 105 +--
opm-0.7-0/opm/R/metadata.R | 36 -
opm-0.7-0/opm/R/naming.R | 25
opm-0.7-0/opm/R/phylogeny.R | 391 +------------
opm-0.7-0/opm/R/plotting.R | 236 +-------
opm-0.7-0/opm/data/vaas_1.rda |binary
opm-0.7-0/opm/data/vaas_4.rda |binary
opm-0.7-0/opm/inst/doc |only
opm-0.7-0/opm/inst/scripts/run_opm.R | 9
opm-0.7-0/opm/man/MOA.Rd | 61 --
opm-0.7-0/opm/man/OPM.Rd | 151 -----
opm-0.7-0/opm/man/OPMA.Rd | 82 --
opm-0.7-0/opm/man/OPMD.Rd |only
opm-0.7-0/opm/man/OPMS.Rd | 210 -------
opm-0.7-0/opm/man/OPMX.Rd | 51 -
opm-0.7-0/opm/man/WMD.Rd | 94 ---
opm-0.7-0/opm/man/YAML_VIA_LIST.Rd | 44 -
opm-0.7-0/opm/man/aggr_settings.Rd | 21
opm-0.7-0/opm/man/aggregated.Rd | 19
opm-0.7-0/opm/man/anyDuplicated.Rd | 55 +
opm-0.7-0/opm/man/best_cutoff.Rd | 8
opm-0.7-0/opm/man/borders.Rd | 10
opm-0.7-0/opm/man/bracket.Rd | 4
opm-0.7-0/opm/man/c.Rd | 4
opm-0.7-0/opm/man/calinski.Rd | 10
opm-0.7-0/opm/man/ci_plot.Rd | 8
opm-0.7-0/opm/man/collect_template.Rd | 2
opm-0.7-0/opm/man/contains.Rd | 9
opm-0.7-0/opm/man/csv_data.Rd | 19
opm-0.7-0/opm/man/dim.Rd | 19
opm-0.7-0/opm/man/disc_settings.Rd |only
opm-0.7-0/opm/man/discrete.Rd | 12
opm-0.7-0/opm/man/discretized.Rd |only
opm-0.7-0/opm/man/do_disc.Rd |only
opm-0.7-0/opm/man/duplicated.Rd | 52 +
opm-0.7-0/opm/man/extract.Rd | 21
opm-0.7-0/opm/man/extract_columns.Rd | 5
opm-0.7-0/opm/man/extract_curve_params.Rd |only
opm-0.7-0/opm/man/filename.Rd | 17
opm-0.7-0/opm/man/flatten.Rd | 15
opm-0.7-0/opm/man/gen_iii.Rd | 3
opm-0.7-0/opm/man/glob_to_regex.Rd | 6
opm-0.7-0/opm/man/has_aggr.Rd | 17
opm-0.7-0/opm/man/has_disc.Rd |only
opm-0.7-0/opm/man/heat_map.Rd | 8
opm-0.7-0/opm/man/hours.Rd | 17
opm-0.7-0/opm/man/include_metadata.Rd | 12
opm-0.7-0/opm/man/initialize.Rd | 16
opm-0.7-0/opm/man/insert.Rd | 4
opm-0.7-0/opm/man/is_constant.Rd | 2
opm-0.7-0/opm/man/is_uniform.Rd | 2
opm-0.7-0/opm/man/kubrick.Rd | 6
opm-0.7-0/opm/man/last.Rd | 2
opm-0.7-0/opm/man/length.Rd | 17
opm-0.7-0/opm/man/level_plot.Rd | 16
opm-0.7-0/opm/man/map_metadata.Rd | 8
opm-0.7-0/opm/man/map_names.Rd | 8
opm-0.7-0/opm/man/map_values.Rd | 4
opm-0.7-0/opm/man/max.Rd | 17
opm-0.7-0/opm/man/measurements.Rd | 17
opm-0.7-0/opm/man/merge.Rd | 7
opm-0.7-0/opm/man/metadata.Rd | 17
opm-0.7-0/opm/man/metadata_chars.Rd | 8
opm-0.7-0/opm/man/minmax.Rd | 17
opm-0.7-0/opm/man/oapply.Rd | 12
opm-0.7-0/opm/man/opm_files.Rd | 4
opm-0.7-0/opm/man/opm_opt.Rd | 4
opm-0.7-0/opm/man/opma_problems.Rd | 4
opm-0.7-0/opm/man/opmd_problems.Rd |only
opm-0.7-0/opm/man/parse_time.Rd | 2
opm-0.7-0/opm/man/phylo_data.Rd | 23
opm-0.7-0/opm/man/plate_type.Rd | 17
opm-0.7-0/opm/man/plates.Rd | 3
opm-0.7-0/opm/man/position.Rd | 17
opm-0.7-0/opm/man/radial_plot.Rd | 4
opm-0.7-0/opm/man/read_opm_yaml.Rd | 5
opm-0.7-0/opm/man/rep.Rd | 3
opm-0.7-0/opm/man/repair_na_strings.Rd | 4
opm-0.7-0/opm/man/rev.Rd | 3
opm-0.7-0/opm/man/run_kmeans.Rd | 44 -
opm-0.7-0/opm/man/safe_labels.Rd | 3
opm-0.7-0/opm/man/select.Rd | 57 +
opm-0.7-0/opm/man/select_colors.Rd | 11
opm-0.7-0/opm/man/separate.Rd | 6
opm-0.7-0/opm/man/seq.Rd | 34 -
opm-0.7-0/opm/man/setup_time.Rd | 17
opm-0.7-0/opm/man/show.Rd | 17
opm-0.7-0/opm/man/sort.Rd | 17
opm-0.7-0/opm/man/substrate_info.Rd | 4
opm-0.7-0/opm/man/summary.Rd | 17
opm-0.7-0/opm/man/thin_out.Rd | 2
opm-0.7-0/opm/man/tidy.Rd | 2
opm-0.7-0/opm/man/to_kmeans.Rd | 9
opm-0.7-0/opm/man/to_yaml.Rd | 6
opm-0.7-0/opm/man/unique.Rd |only
opm-0.7-0/opm/man/vaas_1.Rd | 6
opm-0.7-0/opm/man/vaas_4.Rd | 13
opm-0.7-0/opm/man/well.Rd | 17
opm-0.7-0/opm/man/wells.Rd | 17
opm-0.7-0/opm/man/xy_plot.Rd | 15
opm-0.7-0/opm/vignettes |only
132 files changed, 1689 insertions(+), 2512 deletions(-)
Title: Fitting finite mixture of scale mixture of skew-normal
distributions .
Diff between mixsmsn versions 1.0-2 dated 2012-02-24 and 1.0-3 dated 2012-10-26
Description: Functions to fit finite mixture of scale mixture of
skew-normal (FM-SMSN) distributions.
Author: Marcos Prates
Maintainer: Marcos Prates
ChangeLog | 4 ++++
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/gen.R | 5 +++--
4 files changed, 13 insertions(+), 8 deletions(-)