Title: Create Plots from MCMC Output
Diff between mcmcplots versions 0.3 dated 2011-11-07 and 0.4 dated 2012-10-07
Description: MCMC plots
Author: S. McKay Curtis with contributions from Ilya Goldin
Maintainer: S. McKay Curtis
DESCRIPTION | 13 ++++--
MD5 | 77 +++++++++++++++++++++++-----------------
NAMESPACE | 1
NEWS | 35 +++++++++++++++++-
R/as.mcmc.bugs.R | 20 +++++-----
R/caterplot.R | 52 +++++++++++++++++----------
R/convert.mcmc.list.R |only
R/corplot.R | 11 +++--
R/denoverplot.R | 19 ++++++----
R/denoverplot1.R | 21 +++++++----
R/denplot.R | 32 +++++++++++-----
R/html.begin.R |only
R/html.end.R |only
R/html.img.R |only
R/mcmcplot.R | 78 ++++++++++++++++++++++++++---------------
R/mcmcplot1.R | 29 +++++++--------
R/mcmcplotsPalette.R | 17 ++++++--
R/parms2plot.R | 89 ++++++++++++++++++++++++++++++++++++++---------
R/to.greek.R |only
R/traplot.R | 36 ++++++++++++++-----
R/traplot1.R | 5 ++
inst |only
man/as.mcmc.bugs.Rd | 14 -------
man/as.mcmc.rjags.Rd | 12 +-----
man/autplot1.Rd | 7 +--
man/caterplot.Rd | 30 +++++++++++----
man/caterpoints.Rd | 26 +++----------
man/convert.mcmc.list.Rd |only
man/corplot.Rd | 20 ++++------
man/denoverplot.Rd | 34 ++++++++---------
man/denoverplot1.Rd | 29 +++++++--------
man/denplot.Rd | 33 ++++++++---------
man/graypr.Rd | 14 -------
man/html.begin.Rd |only
man/html.end.Rd |only
man/html.img.Rd |only
man/mcmcplot.Rd | 41 ++++++++++++---------
man/mcmcplot1.Rd | 10 ++---
man/mcmcplots-package.Rd | 16 ++++++--
man/mcmcplotsPalette.Rd | 31 ++++++++++------
man/parcorplot.Rd | 16 ++------
man/parms2plot.Rd | 39 ++++++++++++--------
man/to.greek.Rd |only
man/traplot.Rd | 33 +++++++----------
man/traplot1.Rd | 20 +++-------
45 files changed, 565 insertions(+), 395 deletions(-)
Title: Handy functions for working with HGNC gene symbols and
Affymetrix probeset identifiers.
Diff between HGNChelper versions 0.2 dated 2012-08-16 and 0.2.1 dated 2012-10-07
Description: Contains functions for identifying and correcting HGNC
gene symbols which have been converted to date format by Excel,
for reversibly converting between HGNC symbols and valid R
names, identifying invalid HGNC symbols and correcting synonyms
and outdated symbols which can be mapped to an official symbol.
Author: Levi Waldron and Markus Riester
Maintainer: Levi Waldron
CHANGELOG | 13 +++++++++++--
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/checkGeneSymbols.R | 20 ++++++++++++++------
data/hgnc.table.rda |binary
man/checkGeneSymbols.Rd | 8 ++++++--
6 files changed, 40 insertions(+), 19 deletions(-)
Title: Graphical Interaction Models
Diff between gRim versions 0.1-13 dated 2012-09-10 and 0.1-14 dated 2012-10-07
Description: gRaphical Interaction Models:
Models for for contingency tables (i.e. log-linear models)
Graphical Gaussian models for multivariate normal data (i.e. covariance
selection models)
Mixed interaction models
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
gRim-0.1-13/gRim/R/MI-xxx2yyy.R |only
gRim-0.1-14/gRim/ChangeLog | 8
gRim-0.1-14/gRim/DESCRIPTION | 24
gRim-0.1-14/gRim/MD5 | 19
gRim-0.1-14/gRim/R/MI-fit.R | 71 -
gRim-0.1-14/gRim/R/MI-weakmodel.R | 24
gRim-0.1-14/gRim/R/MI-xxx2yyyParms.R |only
gRim-0.1-14/gRim/R/getEdges.R | 4
gRim-0.1-14/gRim/R/iModel-backwardforward.R | 26
gRim-0.1-14/gRim/gRim-Ex.R | 1135 ++++++++++++++--------------
gRim-0.1-14/gRim/inst/doc/gRim.pdf |binary
gRim-0.1-14/gRim/src/xxx2yyyParms.cpp |only
12 files changed, 649 insertions(+), 662 deletions(-)
Title: A package for graphical modelling in R
Diff between gRbase versions 1.6-3 dated 2012-09-25 and 1.6-4 dated 2012-10-07
Description: The gRbase package provides certain general constructs
which are used by other graphical modelling packages, in
particular by the packages gRain, gRim and gRc.
gRbase contains several datasets relevant for use in connection with
graphical models. Almost all datasets used in the book
Graphical Models with R (2012) are contained in gRbase.
gRbase implements several graph algorithms (based mainly on
representing graphs as adjacency matrices - either in the form
of a standard matrix or a sparse matrix). Some graph algorithms
are: * maximum cardinality search (for marked and unmarked
graphs). * moralize * triangulate * junctionTree
gRbase facilities for array operations,
gRbase implements functions for testing for conditional independence.
gRbase illustrates how hierarchical log-linear models (hllm) may be
implemented and describes concept of gmData (graphical meta
data). These features, however, are not maintained anymore and
remains in gRbase only because there exists a paper describing
these facilities: A Common Platform for Graphical Models in R:
The gRbase Package, Journal of Statistical Software, Vol 14, No
17, 2005.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 9 +++++++++
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++-------
R/GraphAlgo-cliqueMAT.R | 19 ++++++++++++++-----
inst/doc/gRbase-arrayops1.pdf |binary
inst/doc/gRbase-arrayops2.pdf |binary
inst/doc/gRbase-graphs.pdf |binary
inst/doc/gRbase-zzz.pdf |binary
8 files changed, 35 insertions(+), 17 deletions(-)
Title: Conduct univariate and bivariate wavelet analyses
Diff between biwavelet versions 0.11 dated 2012-05-17 and 0.12 dated 2012-10-07
Description: This is a port of the WTC MATLAB package written by Aslak
Grinsted and the wavelet program written by Christopher
Torrence and Gibert P. Compo. This package can be used to
perform univariate and bivariate (cross-wavelet, wavelet
coherence, wavelet clustering) analyses.
Author: Tarik C. Gouhier, Aslak Grinsted
Maintainer: Tarik C. Gouhier
DESCRIPTION | 11 ++++++-----
MD5 | 12 ++++++------
R/plot.biwavelet.R | 45 ++++++++++++++++++++++++++++++++-------------
R/wt.R | 4 ++--
data/enviro.data.RData |binary
man/plot.biwavelet.Rd | 14 ++++++++++++++
man/wclust.Rd | 2 +-
7 files changed, 61 insertions(+), 27 deletions(-)
Title: Tools to manage a parametric function that describes phenology
Diff between phenology versions 3.31 dated 2012-05-15 and 3.40 dated 2012-10-07
Description: Functions to fit and test the phenology of species based
on counts.
Author: Marc Girondot
Maintainer: Marc Girondot
DESCRIPTION | 22 +----
MD5 | 67 +++++++++------
NAMESPACE | 7 +
NEWS | 34 +++++++
R/Likelihood_phenology.R | 47 ++++++----
R/Lnegbin.R | 23 ++---
R/MHalgoGen.R |only
R/Script_MCMC.r |only
R/adapt_parameters.R |only
R/add_format.R | 108 ++++++++++++++++++++----
R/compare_AIC.R | 10 +-
R/daily_count.R | 12 +-
R/fit_phenology.R | 42 ++++-----
R/map_phenology.R | 18 ++--
R/par_init.R | 53 +++++++-----
R/phenology-package.R | 4
R/phenology_MHmcmc_p.R |only
R/phenology_fonctionMCMC.R |only
R/plot.mcmcComposite.R |only
R/plot.phenology.R | 67 ++-------------
R/plot.phenologymap.R | 38 +-------
R/plot_phenology.R | 188 ++++++++++++++++++-------------------------
R/print.phenologyout.R |only
R/result_Gratiot_mcmc.R |only
R/summary.mcmcComposite.R |only
R/summary.phenologyout.R |only
data/result_Gratiot_mcmc.rda |only
man/adapt_parameters.Rd |only
man/add_format.Rd | 22 +++--
man/compare_AIC.Rd | 2
man/fit_phenology.Rd | 16 ++-
man/likelihood_phenology.Rd | 6 -
man/par_init.Rd | 4
man/phenology-package.Rd | 2
man/phenology_MHmcmc.Rd |only
man/phenology_MHmcmc_p.Rd |only
man/plot.mcmcComposite.Rd |only
man/plot.phenology.Rd | 22 ++++-
man/plot.phenologymap.Rd | 16 +++
man/plot_phenology.Rd | 9 +-
man/print.phenologyout.Rd |only
man/result_Gratiot_mcmc.Rd |only
man/summary.mcmcComposite.Rd |only
man/summary.phenologyout.Rd |only
44 files changed, 471 insertions(+), 368 deletions(-)
Title: A multiplatform GUI for drawing customizable graphs in R
Diff between GrapheR versions 1.9-77 dated 2012-03-04 and 1.9-78 dated 2012-10-07
Description: GrapheR is a multiplatform user interface for drawing
highly customizable graphs in R. It aims to be a valuable help
to quickly draw publishable graphs without any knowledge of R
commands. Six kinds of graph are available: histogram,
box-and-whisker plot, bar plot, pie chart, curve and scatter
plot.
Author: Maxime Hervé
Maintainer: Maxime Hervé
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
NEWS | 8 ++++++++
R/Sources.R | 8 ++++----
R/zzzz.R | 2 +-
inst/doc/manual_de.pdf |binary
inst/doc/manual_en.pdf |binary
inst/doc/manual_fr.pdf |binary
man/GrapheR-package.Rd | 4 ++--
9 files changed, 27 insertions(+), 19 deletions(-)
Title: Recursive Partitioning
Diff between rpart versions 3.1-54 dated 2012-06-27 and 3.1-55 dated 2012-10-07
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-3.1-54/rpart/R/formatg.s |only
rpart-3.1-54/rpart/R/labels.rpart.s |only
rpart-3.1-54/rpart/R/meanvar.rpart.s |only
rpart-3.1-54/rpart/R/model.frame.rpart.s |only
rpart-3.1-54/rpart/R/na.rpart.s |only
rpart-3.1-54/rpart/R/path.rpart.s |only
rpart-3.1-54/rpart/R/plot.rpart.s |only
rpart-3.1-54/rpart/R/plotcp.s |only
rpart-3.1-54/rpart/R/post.rpart.s |only
rpart-3.1-54/rpart/R/post.s |only
rpart-3.1-54/rpart/R/pred.rpart.s |only
rpart-3.1-54/rpart/R/predict.rpart.s |only
rpart-3.1-54/rpart/R/print.rpart.s |only
rpart-3.1-54/rpart/R/printcp.s |only
rpart-3.1-54/rpart/R/prune.rpart.s |only
rpart-3.1-54/rpart/R/prune.s |only
rpart-3.1-54/rpart/R/residuals.rpart.s |only
rpart-3.1-54/rpart/R/rpart.anova.s |only
rpart-3.1-54/rpart/R/rpart.branch.s |only
rpart-3.1-54/rpart/R/rpart.class.s |only
rpart-3.1-54/rpart/R/rpart.control.s |only
rpart-3.1-54/rpart/R/rpart.exp.s |only
rpart-3.1-54/rpart/R/rpart.matrix.s |only
rpart-3.1-54/rpart/R/rpart.poisson.s |only
rpart-3.1-54/rpart/R/rpart.s |only
rpart-3.1-54/rpart/R/rpartcallback.s |only
rpart-3.1-54/rpart/R/rpartco.s |only
rpart-3.1-54/rpart/R/rpconvert.s |only
rpart-3.1-54/rpart/R/rsq.rpart.s |only
rpart-3.1-54/rpart/R/snip.rpart.mouse.s |only
rpart-3.1-54/rpart/R/snip.rpart.s |only
rpart-3.1-54/rpart/R/summary.rpart.s |only
rpart-3.1-54/rpart/R/text.rpart.s |only
rpart-3.1-54/rpart/R/xpred.rpart.s |only
rpart-3.1-54/rpart/data/car.test.frame.csv.gz |only
rpart-3.1-54/rpart/data/kyphosis.tab.gz |only
rpart-3.1-54/rpart/data/solder.tab.gz |only
rpart-3.1-54/rpart/po/R-en@quot.po |only
rpart-3.1-54/rpart/po/en@quot.po |only
rpart-3.1-55/rpart/ChangeLog | 9
rpart-3.1-55/rpart/DESCRIPTION | 25
rpart-3.1-55/rpart/MD5 | 200 ++---
rpart-3.1-55/rpart/R/formatg.R |only
rpart-3.1-55/rpart/R/labels.rpart.R |only
rpart-3.1-55/rpart/R/meanvar.rpart.R |only
rpart-3.1-55/rpart/R/model.frame.rpart.R |only
rpart-3.1-55/rpart/R/na.rpart.R |only
rpart-3.1-55/rpart/R/path.rpart.R |only
rpart-3.1-55/rpart/R/plot.rpart.R |only
rpart-3.1-55/rpart/R/plotcp.R |only
rpart-3.1-55/rpart/R/post.R |only
rpart-3.1-55/rpart/R/post.rpart.R |only
rpart-3.1-55/rpart/R/pred.rpart.R |only
rpart-3.1-55/rpart/R/predict.rpart.R |only
rpart-3.1-55/rpart/R/print.rpart.R |only
rpart-3.1-55/rpart/R/printcp.R |only
rpart-3.1-55/rpart/R/prune.R |only
rpart-3.1-55/rpart/R/prune.rpart.R |only
rpart-3.1-55/rpart/R/residuals.rpart.R |only
rpart-3.1-55/rpart/R/rpart.R |only
rpart-3.1-55/rpart/R/rpart.anova.R |only
rpart-3.1-55/rpart/R/rpart.branch.R |only
rpart-3.1-55/rpart/R/rpart.class.R |only
rpart-3.1-55/rpart/R/rpart.control.R |only
rpart-3.1-55/rpart/R/rpart.exp.R |only
rpart-3.1-55/rpart/R/rpart.matrix.R |only
rpart-3.1-55/rpart/R/rpart.poisson.R |only
rpart-3.1-55/rpart/R/rpartcallback.R |only
rpart-3.1-55/rpart/R/rpartco.R |only
rpart-3.1-55/rpart/R/rpconvert.R |only
rpart-3.1-55/rpart/R/rsq.rpart.R |only
rpart-3.1-55/rpart/R/snip.rpart.R |only
rpart-3.1-55/rpart/R/snip.rpart.mouse.R |only
rpart-3.1-55/rpart/R/summary.rpart.R |only
rpart-3.1-55/rpart/R/text.rpart.R |only
rpart-3.1-55/rpart/R/xpred.rpart.R |only
rpart-3.1-55/rpart/R/zzz.R | 8
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/inst/po/de/LC_MESSAGES/R-rpart.mo |binary
rpart-3.1-55/rpart/inst/po/de/LC_MESSAGES/rpart.mo |binary
rpart-3.1-55/rpart/inst/po/en@quot/LC_MESSAGES/R-rpart.mo |binary
rpart-3.1-55/rpart/inst/po/en@quot/LC_MESSAGES/rpart.mo |binary
rpart-3.1-55/rpart/inst/po/fr/LC_MESSAGES/R-rpart.mo |binary
rpart-3.1-55/rpart/inst/po/fr/LC_MESSAGES/rpart.mo |binary
rpart-3.1-55/rpart/inst/po/pl/LC_MESSAGES/R-rpart.mo |binary
rpart-3.1-55/rpart/inst/po/pl/LC_MESSAGES/rpart.mo |binary
rpart-3.1-55/rpart/inst/po/ru/LC_MESSAGES/R-rpart.mo |binary
rpart-3.1-55/rpart/inst/po/ru/LC_MESSAGES/rpart.mo |binary
rpart-3.1-55/rpart/man/rpart.Rd | 11
rpart-3.1-55/rpart/man/rpart.control.Rd | 3
rpart-3.1-55/rpart/man/text.rpart.Rd | 22
rpart-3.1-55/rpart/po/R-de.po | 205 +++---
rpart-3.1-55/rpart/po/R-fr.po | 195 +++--
rpart-3.1-55/rpart/po/R-pl.po | 471 ++++++++++----
rpart-3.1-55/rpart/po/R-rpart.pot | 118 +--
rpart-3.1-55/rpart/po/R-ru.po | 212 +++---
rpart-3.1-55/rpart/po/de.po | 26
rpart-3.1-55/rpart/po/fr.po | 26
rpart-3.1-55/rpart/po/pl.po | 58 +
rpart-3.1-55/rpart/po/rpart.pot | 30
rpart-3.1-55/rpart/po/ru.po | 26
rpart-3.1-55/rpart/src/anova.c | 1
rpart-3.1-55/rpart/src/anovapred.c | 1
rpart-3.1-55/rpart/src/branch.c | 1
rpart-3.1-55/rpart/src/bsplit.c | 1
rpart-3.1-55/rpart/src/choose_surg.c | 1
rpart-3.1-55/rpart/src/fix_cp.c | 1
rpart-3.1-55/rpart/src/free_tree.c | 1
rpart-3.1-55/rpart/src/func_table.h | 1
rpart-3.1-55/rpart/src/gini.c | 2
rpart-3.1-55/rpart/src/graycode.c | 1
rpart-3.1-55/rpart/src/init.c | 4
rpart-3.1-55/rpart/src/insert_split.c | 1
rpart-3.1-55/rpart/src/make_cp_list.c | 1
rpart-3.1-55/rpart/src/make_cp_table.c | 1
rpart-3.1-55/rpart/src/mysort.c | 1
rpart-3.1-55/rpart/src/node.h | 1
rpart-3.1-55/rpart/src/nodesplit.c | 1
rpart-3.1-55/rpart/src/partition.c | 1
rpart-3.1-55/rpart/src/poisson.c | 1
rpart-3.1-55/rpart/src/pred_rpart.c | 1
rpart-3.1-55/rpart/src/rpart.c | 1
rpart-3.1-55/rpart/src/rpart.h | 1
rpart-3.1-55/rpart/src/rpartS.h | 1
rpart-3.1-55/rpart/src/rpart_callback.c | 1
rpart-3.1-55/rpart/src/rpartexp2.c | 1
rpart-3.1-55/rpart/src/rpartproto.h | 1
rpart-3.1-55/rpart/src/rpcountup.c | 1
rpart-3.1-55/rpart/src/rpmatrix.c | 1
rpart-3.1-55/rpart/src/rundown.c | 1
rpart-3.1-55/rpart/src/rundown2.c | 1
rpart-3.1-55/rpart/src/s_to_rp.c | 1
rpart-3.1-55/rpart/src/s_xpred.c | 1
rpart-3.1-55/rpart/src/surrogate.c | 1
rpart-3.1-55/rpart/src/usersplit.c | 1
rpart-3.1-55/rpart/src/xval.c | 1
rpart-3.1-55/rpart/tests/Examples/rpart-Ex.Rout.save | 2
139 files changed, 996 insertions(+), 690 deletions(-)