Title: Group Sequential Design in Equivalence Studies
Diff between gset versions 1.0 dated 2014-05-19 and 1.1.0 dated 2014-11-19
Description: calculate equivalence and futility boundaries based on the exact bivariate $t$ test statistics for group sequential designs in studies with equivalence hypotheses.
Author: Fang Liu [aut, cre]
Maintainer: Fang Liu
DESCRIPTION | 10 +++++-----
MD5 | 30 ++++++++++++++++--------------
R/binding.R | 4 ++--
R/equivonly.R | 4 +++-
R/nminmax.R | 6 +++---
R/nonbinding.R | 4 +++-
man/binding.Rd | 10 +++++++---
man/equivonly.Rd | 10 +++++++---
man/figureE.Rd | 4 +++-
man/figureEF.Rd | 4 +++-
man/gset-package.Rd | 8 +++++---
man/nfix.Rd | 4 +++-
man/nminmax.Rd | 8 ++++++--
man/nonbinding.Rd | 10 +++++++---
man/oc.Rd | 4 +++-
tests |only
16 files changed, 76 insertions(+), 44 deletions(-)
Title: Tau-leaping stochastic simulation
Diff between adaptivetau versions 2.1 dated 2014-05-08 and 2.2 dated 2014-11-19
Description: Implements adaptive tau leaping to approximate the
trajectory of a continuous-time stochastic process as
described by Cao et al. (2007) The Journal of Chemical
Physics. This package is based upon work supported by
NSF DBI-0906041 and NIH K99-GM104158 to Philip Johnson and
NIH R01-AI049334 to Rustom Antia.
Author: Philip Johnson
Maintainer: Philip Johnson
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
NEWS | 7 +++++++
build/vignette.rds |binary
inst/doc/adaptivetau.R | 4 ++--
inst/doc/adaptivetau.Rnw | 6 +++---
inst/doc/adaptivetau.pdf |binary
man/ssa.adaptivetau.Rd | 9 ++++++---
man/ssa.exact.Rd | 9 ++++++---
src/adaptivetau.cpp | 38 +++++++++++++++++++++++++++++---------
vignettes/adaptivetau.Rnw | 6 +++---
11 files changed, 70 insertions(+), 37 deletions(-)
Title: Meta-Analysis with R
Diff between meta versions 3.8-0 dated 2014-09-12 and 4.0-1 dated 2014-11-19
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package metafor is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer
meta-3.8-0/meta/R/addvar.R |only
meta-3.8-0/meta/man/addvar.Rd |only
meta-4.0-1/meta/DESCRIPTION | 8
meta-4.0-1/meta/MD5 | 123 -
meta-4.0-1/meta/NAMESPACE | 3
meta-4.0-1/meta/NEWS | 75
meta-4.0-1/meta/R/as.data.frame.meta.R | 13
meta-4.0-1/meta/R/baujat.meta.R | 21
meta-4.0-1/meta/R/bubble.metareg.R | 60
meta-4.0-1/meta/R/bylevs.R |only
meta-4.0-1/meta/R/byvarname.R |only
meta-4.0-1/meta/R/catmeth.R | 2
meta-4.0-1/meta/R/chkchar.R |only
meta-4.0-1/meta/R/chkclass.R |only
meta-4.0-1/meta/R/chklength.R |only
meta-4.0-1/meta/R/chklevel.R |only
meta-4.0-1/meta/R/chklogical.R |only
meta-4.0-1/meta/R/chkmetafor.R |only
meta-4.0-1/meta/R/chkmiss.R |only
meta-4.0-1/meta/R/chknull.R |only
meta-4.0-1/meta/R/chknumeric.R |only
meta-4.0-1/meta/R/forest.meta.R | 2284 +++++++++++++-----------------
meta-4.0-1/meta/R/format.p.R | 20
meta-4.0-1/meta/R/format.tau.R | 11
meta-4.0-1/meta/R/funnel.default.R | 285 ---
meta-4.0-1/meta/R/funnel.meta.R | 180 +-
meta-4.0-1/meta/R/hetcalc.R |only
meta-4.0-1/meta/R/int2num.R |only
meta-4.0-1/meta/R/labbe.metabin.R | 13
meta-4.0-1/meta/R/metabias.meta.R | 11
meta-4.0-1/meta/R/metabias.rm5.R | 10
meta-4.0-1/meta/R/metabin.R | 761 ++++-----
meta-4.0-1/meta/R/metacont.R | 494 +++---
meta-4.0-1/meta/R/metacor.R | 429 ++---
meta-4.0-1/meta/R/metacr.R | 88 -
meta-4.0-1/meta/R/metacum.R | 291 +--
meta-4.0-1/meta/R/metagen.R | 587 +++----
meta-4.0-1/meta/R/metainc.R | 713 ++++-----
meta-4.0-1/meta/R/metainf.R | 287 +--
meta-4.0-1/meta/R/metaprop.R | 533 +++----
meta-4.0-1/meta/R/metareg.R | 20
meta-4.0-1/meta/R/npn.R |only
meta-4.0-1/meta/R/paulemandel.R | 2
meta-4.0-1/meta/R/print.meta.R | 163 +-
meta-4.0-1/meta/R/print.metabias.R | 12
meta-4.0-1/meta/R/print.rm5.R | 12
meta-4.0-1/meta/R/print.summary.meta.R | 465 ++----
meta-4.0-1/meta/R/print.summary.rm5.R | 10
meta-4.0-1/meta/R/radial.meta.R | 10
meta-4.0-1/meta/R/read.rm5.R | 24
meta-4.0-1/meta/R/setchar.R |only
meta-4.0-1/meta/R/setstudlab.R |only
meta-4.0-1/meta/R/settings.meta.R | 187 --
meta-4.0-1/meta/R/subgroup.R |only
meta-4.0-1/meta/R/summary.meta.R | 495 +-----
meta-4.0-1/meta/R/summary.rm5.R | 19
meta-4.0-1/meta/R/trimfill.default.R | 37
meta-4.0-1/meta/R/trimfill.meta.R | 78 -
meta-4.0-1/meta/R/update.meta.R | 175 +-
meta-4.0-1/meta/R/updateversion.R |only
meta-4.0-1/meta/man/as.data.frame.meta.Rd |only
meta-4.0-1/meta/man/forest.Rd | 132 +
meta-4.0-1/meta/man/funnel.Rd | 6
meta-4.0-1/meta/man/metabin.Rd | 70
meta-4.0-1/meta/man/metacont.Rd | 66
meta-4.0-1/meta/man/metacor.Rd | 66
meta-4.0-1/meta/man/metacr.Rd | 5
meta-4.0-1/meta/man/metacum.Rd | 8
meta-4.0-1/meta/man/metagen.Rd | 66
meta-4.0-1/meta/man/metainc.Rd | 70
meta-4.0-1/meta/man/metainf.Rd | 11
meta-4.0-1/meta/man/metaprop.Rd | 70
meta-4.0-1/meta/man/print.meta.Rd | 6
73 files changed, 4559 insertions(+), 5028 deletions(-)
Title: Co-correspondence Analysis Methods
Diff between cocorresp versions 0.2-1 dated 2013-12-13 and 0.2-3 dated 2014-11-19
Description: Fits predictive and symmetric co-correspondence analysis (CoCA) models to relate one data matrix
to another data matrix. More specifically, CoCA maximises the weighted covariance
between the weighted averaged species scores of one community and the weighted averaged species
scores of another community. CoCA attempts to find patterns that are common to both communities.
Author: Original Matlab routines by C.J.F. ter Braak and A.P. Schaffers. R port by Gavin L. Simpson.
Function simpls based on simpls.fit (package pls) by Ron Wehrens and Bjorn-Helge Mevik.
Maintainer: Gavin L. Simpson
DESCRIPTION | 19 ++++------
MD5 | 63 +++++++++++++++++-----------------
NAMESPACE | 3 +
R/coca.formula.R | 2 -
R/coinertiaI.R | 31 +++++++---------
R/crossval.R | 10 ++---
R/envfit.coca.R | 2 -
R/fitCoinertia.R | 2 -
R/mcChi.R | 3 +
R/permutest.coca.R | 2 -
R/print.coinertia.R | 1
R/print.crossval.R | 1
R/print.fitted.symcoca.R | 1
R/print.permutest.coca.R | 1
R/print.summary.coinertia.R | 1
R/print.summary.crossval.R | 1
R/print.summary.permutest.coca.R | 1
R/print.summary.predcoca.R | 1
R/print.summary.symcoca.R | 1
R/rescale.symcoca.R | 2 -
R/scaleChi.R | 4 +-
R/simpls.R | 3 +
R/summary.crossval.R | 2 -
R/summary.symcoca.R | 2 -
README.md |only
data/beetles.rda |binary
data/bryophyte.rda |binary
data/plants.rda |binary
data/vascular.rda |binary
inst/ChangeLog | 19 ++++++++++
man/envfit.coca.Rd | 2 -
man/permutest.coca.Rd | 3 +
tests/Examples/cocorresp-Ex.Rout.save | 16 ++++----
33 files changed, 115 insertions(+), 84 deletions(-)
Title: Utilities for working with SQL files.
Diff between sqlutils versions 1.1.2 dated 2014-05-02 and 1.2 dated 2014-11-19
Description: This package provides utilities for working with a library of SQL
files.
Author: Jason Bryer
Maintainer: Jason Bryer
DESCRIPTION | 11 ++--
MD5 | 84 ++++++++++++++++++---------------
NAMESPACE | 6 --
NEWS | 4 +
R/cacheQuery.r | 28 -----------
R/execQuery.r |only
R/getCacheFilename.r |only
R/getSQL.r | 14 -----
R/getSQLRaw.r |only
R/interactiveSQL.r | 7 ++
R/recodeColumns.r |only
R/sqlFile.r |only
R/sqlPaths.r | 18 -------
R/sqldoc.r | 3 +
R/sqlexec.R | 90 ++++++++----------------------------
build/vignette.rds |binary
inst/doc/DataDictionary.R | 6 +-
inst/doc/DataDictionary.Rnw | 9 +--
inst/doc/DataDictionary.pdf |binary
inst/sql/StudentSummary.sql | 6 +-
inst/sql/StudentsInRange.sql | 16 +++---
man/cacheQuery.Rd | 2
man/execQuery.Rd | 2
man/getCacheFilename.Rd | 2
man/getParameters.Rd | 2
man/getQueries.Rd | 2
man/getSQL.Rd | 2
man/getSQLRaw.Rd | 2
man/is.null.string.Rd | 2
man/isql.Rd | 2
man/parse.element.Rd | 2
man/parse.introduction.Rd | 2
man/print.Rd | 2
man/recodeColumns.Rd | 2
man/sqlFile.Rd | 2
man/sqlPaths.Rd | 4 -
man/sqldoc.Rd | 2
man/sqlexec.JDBCConnection.Rd |only
man/sqlexec.PostgreSQLConnection.Rd | 5 --
man/sqlexec.RMySQL.Rd | 5 --
man/sqlexec.RODBC.Rd | 5 --
man/sqlexec.Rd | 2
man/sqlexec.SQLiteConnection.Rd | 5 --
man/sqlutils-package.Rd | 2
man/sqlutils.envir.Rd | 4 -
vignettes/DataDictionary.Rnw | 9 +--
46 files changed, 134 insertions(+), 239 deletions(-)
Title: Data Visualization for Statistics in Social Science
Diff between sjPlot versions 1.5 dated 2014-09-10 and 1.6 dated 2014-11-19
Description: Collection of several plotting / table output functions for
visualizing data and utility functions.
Author: Daniel Lüdecke
Maintainer: Daniel Luedecke
sjPlot-1.5/sjPlot/man/sju.aov1.levene.Rd |only
sjPlot-1.6/sjPlot/DESCRIPTION | 12
sjPlot-1.6/sjPlot/MD5 | 220 +-
sjPlot-1.6/sjPlot/NAMESPACE | 184 +-
sjPlot-1.6/sjPlot/NEWS | 729 ++++----
sjPlot-1.6/sjPlot/R/efc.R | 20
sjPlot-1.6/sjPlot/R/helpfunctions.R | 273 +++
sjPlot-1.6/sjPlot/R/sjImportSPSS.R | 163 +
sjPlot-1.6/sjPlot/R/sjPlotAncovaLSMeans.R | 881 ++++------
sjPlot-1.6/sjPlot/R/sjPlotAnova.R | 1251 ++++++--------
sjPlot-1.6/sjPlot/R/sjPlotClusterAnalysis.R | 1999 ++++++++++-------------
sjPlot-1.6/sjPlot/R/sjPlotCorr.R | 838 ++++-----
sjPlot-1.6/sjPlot/R/sjPlotFrequencies.R | 1968 +++++++++-------------
sjPlot-1.6/sjPlot/R/sjPlotGLME.R |only
sjPlot-1.6/sjPlot/R/sjPlotGroupFrequencies.R | 806 +++------
sjPlot-1.6/sjPlot/R/sjPlotInteractions.R | 1479 +++++++----------
sjPlot-1.6/sjPlot/R/sjPlotLikert.R | 1044 +++++-------
sjPlot-1.6/sjPlot/R/sjPlotLinreg.R | 2155 ++++++++++---------------
sjPlot-1.6/sjPlot/R/sjPlotLinregMultiple.R | 1011 ++++-------
sjPlot-1.6/sjPlot/R/sjPlotOdds.R | 1599 +++++++++---------
sjPlot-1.6/sjPlot/R/sjPlotOddsMultiple.R | 1031 ++++-------
sjPlot-1.6/sjPlot/R/sjPlotPCA.R | 303 ---
sjPlot-1.6/sjPlot/R/sjPlotPearsonsChi2Test.R | 70
sjPlot-1.6/sjPlot/R/sjPlotPropTable.R | 1584 ++++++++----------
sjPlot-1.6/sjPlot/R/sjPlotScatter.R | 782 +++------
sjPlot-1.6/sjPlot/R/sjPlotSetTheme.R |only
sjPlot-1.6/sjPlot/R/sjPlotStackFrequencies.R | 1117 +++++-------
sjPlot-1.6/sjPlot/R/sjRecode.R | 89 -
sjPlot-1.6/sjPlot/R/sjStatistics.R | 173 +-
sjPlot-1.6/sjPlot/R/sjTabCorr.R | 56
sjPlot-1.6/sjPlot/R/sjTabDataFrame.R | 67
sjPlot-1.6/sjPlot/R/sjTabFrequencies.R | 179 --
sjPlot-1.6/sjPlot/R/sjTabGrpmean.R |only
sjPlot-1.6/sjPlot/R/sjTabItemAnalysis.R | 853 ++++-----
sjPlot-1.6/sjPlot/R/sjTabLinReg.R | 180 +-
sjPlot-1.6/sjPlot/R/sjTabOdds.R | 1389 ++++++++--------
sjPlot-1.6/sjPlot/R/sjTabPCA.R | 60
sjPlot-1.6/sjPlot/R/sjTabPropTable.R | 98 -
sjPlot-1.6/sjPlot/R/sjTabSPSS.R | 680 +++----
sjPlot-1.6/sjPlot/R/sjTabStackFrq.R | 1070 ++++++------
sjPlot-1.6/sjPlot/README.md | 60
sjPlot-1.6/sjPlot/man/efc.Rd | 84
sjPlot-1.6/sjPlot/man/sj.setGeomColors.Rd |only
sjPlot-1.6/sjPlot/man/sjPlot-package.Rd | 12
sjPlot-1.6/sjPlot/man/sjc.cluster.Rd | 195 +-
sjPlot-1.6/sjPlot/man/sjc.dend.Rd | 110 -
sjPlot-1.6/sjPlot/man/sjc.elbow.Rd | 75
sjPlot-1.6/sjPlot/man/sjc.grpdisc.Rd | 112 -
sjPlot-1.6/sjPlot/man/sjc.kgap.Rd | 154 -
sjPlot-1.6/sjPlot/man/sjc.qclus.Rd | 543 ++----
sjPlot-1.6/sjPlot/man/sji.SPSS.Rd | 45
sjPlot-1.6/sjPlot/man/sji.convertToLabel.Rd | 75
sjPlot-1.6/sjPlot/man/sji.convertToValue.Rd | 72
sjPlot-1.6/sjPlot/man/sji.getValueLabels.Rd | 33
sjPlot-1.6/sjPlot/man/sji.getVariableLabels.Rd | 32
sjPlot-1.6/sjPlot/man/sji.setValueLabels.Rd | 45
sjPlot-1.6/sjPlot/man/sji.setVariableLabels.Rd | 43
sjPlot-1.6/sjPlot/man/sji.viewSPSS.Rd | 187 --
sjPlot-1.6/sjPlot/man/sjp.aov1.Rd | 462 +----
sjPlot-1.6/sjPlot/man/sjp.chi2.Rd | 175 --
sjPlot-1.6/sjPlot/man/sjp.corr.Rd | 361 +---
sjPlot-1.6/sjPlot/man/sjp.emm.int.Rd | 389 +---
sjPlot-1.6/sjPlot/man/sjp.frq.Rd | 738 +++-----
sjPlot-1.6/sjPlot/man/sjp.glm.Rd | 502 ++---
sjPlot-1.6/sjPlot/man/sjp.glm.ma.Rd | 74
sjPlot-1.6/sjPlot/man/sjp.glmer.Rd |only
sjPlot-1.6/sjPlot/man/sjp.glmm.Rd | 473 +----
sjPlot-1.6/sjPlot/man/sjp.grpfrq.Rd | 787 +++------
sjPlot-1.6/sjPlot/man/sjp.likert.Rd | 554 ++----
sjPlot-1.6/sjPlot/man/sjp.lm.Rd | 387 +---
sjPlot-1.6/sjPlot/man/sjp.lm.int.Rd | 495 +----
sjPlot-1.6/sjPlot/man/sjp.lm.ma.Rd | 84
sjPlot-1.6/sjPlot/man/sjp.lm1.Rd | 314 +--
sjPlot-1.6/sjPlot/man/sjp.lmer.Rd |only
sjPlot-1.6/sjPlot/man/sjp.lmm.Rd | 372 +---
sjPlot-1.6/sjPlot/man/sjp.pca.Rd | 398 +---
sjPlot-1.6/sjPlot/man/sjp.reglin.Rd | 195 +-
sjPlot-1.6/sjPlot/man/sjp.scatter.Rd | 426 +---
sjPlot-1.6/sjPlot/man/sjp.setTheme.Rd |only
sjPlot-1.6/sjPlot/man/sjp.stackfrq.Rd | 367 +---
sjPlot-1.6/sjPlot/man/sjp.vif.Rd | 56
sjPlot-1.6/sjPlot/man/sjp.xtab.Rd | 498 +----
sjPlot-1.6/sjPlot/man/sjs.aov1.levene.Rd |only
sjPlot-1.6/sjPlot/man/sjs.betaCoef.Rd | 82
sjPlot-1.6/sjPlot/man/sjs.chi2.gof.Rd | 82
sjPlot-1.6/sjPlot/man/sjs.cramer.Rd | 52
sjPlot-1.6/sjPlot/man/sjs.cronbach.Rd | 56
sjPlot-1.6/sjPlot/man/sjs.etasq.Rd |only
sjPlot-1.6/sjPlot/man/sjs.mic.Rd | 95 -
sjPlot-1.6/sjPlot/man/sjs.mwu.Rd | 114 -
sjPlot-1.6/sjPlot/man/sjs.phi.Rd | 52
sjPlot-1.6/sjPlot/man/sjs.reliability.Rd | 173 +-
sjPlot-1.6/sjPlot/man/sjs.se.Rd |only
sjPlot-1.6/sjPlot/man/sjs.table.values.Rd | 79
sjPlot-1.6/sjPlot/man/sjt.corr.Rd | 388 ++--
sjPlot-1.6/sjPlot/man/sjt.df.Rd | 229 +-
sjPlot-1.6/sjPlot/man/sjt.frq.Rd | 463 ++---
sjPlot-1.6/sjPlot/man/sjt.glm.Rd | 394 ++--
sjPlot-1.6/sjPlot/man/sjt.grpmean.Rd |only
sjPlot-1.6/sjPlot/man/sjt.itemanalysis.Rd | 331 +--
sjPlot-1.6/sjPlot/man/sjt.lm.Rd | 422 ++--
sjPlot-1.6/sjPlot/man/sjt.pca.Rd | 389 ++--
sjPlot-1.6/sjPlot/man/sjt.stackfrq.Rd | 255 +-
sjPlot-1.6/sjPlot/man/sjt.xtab.Rd | 491 ++---
sjPlot-1.6/sjPlot/man/sju.adjustPlotRange.y.Rd | 91 -
sjPlot-1.6/sjPlot/man/sju.dicho.Rd | 78
sjPlot-1.6/sjPlot/man/sju.groupString.Rd | 101 -
sjPlot-1.6/sjPlot/man/sju.groupVar.Rd | 141 -
sjPlot-1.6/sjPlot/man/sju.groupVarLabels.Rd | 160 -
sjPlot-1.6/sjPlot/man/sju.mean.n.Rd | 76
sjPlot-1.6/sjPlot/man/sju.recode.Rd | 47
sjPlot-1.6/sjPlot/man/sju.recodeTo.Rd | 97 -
sjPlot-1.6/sjPlot/man/sju.setNA.Rd | 62
sjPlot-1.6/sjPlot/man/sju.strpos.Rd | 137 -
sjPlot-1.6/sjPlot/man/sju.weight.Rd | 78
sjPlot-1.6/sjPlot/man/sju.weight2.Rd | 92 -
sjPlot-1.6/sjPlot/man/sju.wordwrap.Rd | 58
117 files changed, 18196 insertions(+), 23566 deletions(-)
Title: Plot rpart models. An enhanced version of plot.rpart.
Diff between rpart.plot versions 1.4-4 dated 2014-02-05 and 1.4-5 dated 2014-11-19
Description: Plot rpart models. Extends plot.rpart and text.rpart in
the rpart package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow
DESCRIPTION | 6
MD5 | 21
NEWS | 6
inst/doc/prp.pdf |binary
inst/slowtests/make.bat | 2
inst/slowtests/test.prp.R | 22
inst/slowtests/test.prp.Rout.save | 43
inst/slowtests/test.prp.save.ps |30479 ++++++++++++++++++++------------------
inst/slowtests/user-manual-figs.R | 27
inst/slowtests/webpage-figs.R |only
man/prp.Rd | 14
man/rpart.plot.Rd | 8
12 files changed, 16664 insertions(+), 13964 deletions(-)
Title: Pedometric Tools and Techniques
Diff between pedometrics versions 0.1-9 dated 2014-08-08 and 0.3-0 dated 2014-11-19
Description: This package contains functions to employ many tools and techniques used in the field of pedometrics (see http://en.wikipedia.org/wiki/Pedometrics for definition of pedometrics). These functions were developed to fulfil the demands created by the PhD research project (2012-2016) entitled Contribution to the Construction of Models for Predicting Soil Properties, developed by Alessandro Samuel-Rosa under the supervision of Dr Lucia HC Anjos (Universidade Federal Rural do Rio de Janeiro, Brazil), Dr Gustavo M Vasques (Embrapa Solos, Brazil), and Dr Gerard BM Heuvelink (ISRIC - World Soil Information, the Netherlands). The project is supported by the CAPES, Ministério da Educação, Brasília - DF 70040-020, Brazil, process ID BEX 11677/13-9. Several functions are simple wrapper functions that extend the functionalities of other functions commonly used for the analysis of pedometric data. It should be noted that changes are likely to occur quite often and using this package as a dependency for other packages is strongly discouraged.
Author: Alessandro Samuel-Rosa [aut, cre], Lucia Helena Cunha dos Anjos [ths], Gustavo de Mattos Vasques [ths], Gerard B. M. Heuvelink [ths], Tony Olsen [ctb], Tom Kincaid [ctb], Juan Carlos Ruiz Cuetos [ctb], Maria Eugenia Polo Garcia [ctb], Pablo Garcia Rodriguez [ctb], Edzer Pebesma [ctb], Jon Skoien [ctb]
Maintainer: Alessandro Samuel-Rosa
pedometrics-0.1-9/pedometrics/inst/CITATION |only
pedometrics-0.3-0/pedometrics/DESCRIPTION | 38 +++++++-----
pedometrics-0.3-0/pedometrics/MD5 | 27 ++++++---
pedometrics-0.3-0/pedometrics/NAMESPACE | 43 +++++++++-----
pedometrics-0.3-0/pedometrics/R/bbox2sp.R |only
pedometrics-0.3-0/pedometrics/R/buildMS.R | 19 ------
pedometrics-0.3-0/pedometrics/R/objMSSD.R |only
pedometrics-0.3-0/pedometrics/R/objectiveLags.R |only
pedometrics-0.3-0/pedometrics/R/plotESDA.R |only
pedometrics-0.3-0/pedometrics/R/plotHD.R |only
pedometrics-0.3-0/pedometrics/R/spJitter.R |only
pedometrics-0.3-0/pedometrics/R/spSANN.R |only
pedometrics-0.3-0/pedometrics/inst/NEWS.Rd | 45 +++++++++++++++
pedometrics-0.3-0/pedometrics/man/bbox2sp.Rd |only
pedometrics-0.3-0/pedometrics/man/coordenadas.Rd | 2
pedometrics-0.3-0/pedometrics/man/objMSSD.Rd |only
pedometrics-0.3-0/pedometrics/man/objectiveLags.Rd |only
pedometrics-0.3-0/pedometrics/man/pedometrics-package.Rd | 12 ++--
pedometrics-0.3-0/pedometrics/man/plotESDA.Rd |only
pedometrics-0.3-0/pedometrics/man/plotHD.Rd |only
pedometrics-0.3-0/pedometrics/man/spJitter.Rd |only
pedometrics-0.3-0/pedometrics/man/spSANN.Rd |only
22 files changed, 124 insertions(+), 62 deletions(-)
Title: Population (and individual) optimal Experimental Design
Diff between PopED versions 0.1.1 dated 2014-05-27 and 0.1.2 dated 2014-11-19
Description: PopED computes optimal experimental designs for both population
studies and individual studies based on nonlinear mixed-effect models.
Often this is based on a computation of the Fisher Information Matrix
(FIM).
Author: Andrew C. Hooker [aut, cre, trl, cph],
Sebastian Ueckert [aut] (MATLAB version),
Marco Foracchia [aut] (O-Matrix version),
Joakim Nyberg [aut] (MATLAB version),
Eric Stroemberg [ctb] (MATLAB version)
Maintainer: Andrew C. Hooker
PopED-0.1.1/PopED/inst/examples/ex.2.d.warfarin.ODE.R |only
PopED-0.1.1/PopED/tests/testthat/test_create.poped.database.R |only
PopED-0.1.2/PopED/DESCRIPTION | 47 -
PopED-0.1.2/PopED/MD5 | 269 +++++----
PopED-0.1.2/PopED/NAMESPACE | 2
PopED-0.1.2/PopED/NEWS | 37 +
PopED-0.1.2/PopED/R/Doptim.R | 18
PopED-0.1.2/PopED/R/RS_opt_gen.R | 4
PopED-0.1.2/PopED/R/build_sfg.R |only
PopED-0.1.2/PopED/R/convert_variables.R | 220 -------
PopED-0.1.2/PopED/R/create.poped.database.R | 277 +++++++---
PopED-0.1.2/PopED/R/create_design.R |only
PopED-0.1.2/PopED/R/create_design_space.R |only
PopED-0.1.2/PopED/R/ed_laplace_ofv.R | 28 -
PopED-0.1.2/PopED/R/evaluate.e.ofv.fim.R | 2
PopED-0.1.2/PopED/R/evaluate.fim.R | 19
PopED-0.1.2/PopED/R/feval.R | 6
PopED-0.1.2/PopED/R/get_all_params.R | 42 -
PopED-0.1.2/PopED/R/get_fim_size.R | 24
PopED-0.1.2/PopED/R/getfulld.R | 26
PopED-0.1.2/PopED/R/log_prior_pdf.R | 2
PopED-0.1.2/PopED/R/m1.R | 29 -
PopED-0.1.2/PopED/R/model_prediction.R |only
PopED-0.1.2/PopED/R/ofv_criterion.R | 1
PopED-0.1.2/PopED/R/plot_efficiency_of_windows.R | 70 ++
PopED-0.1.2/PopED/R/plot_model_prediction.R | 247 --------
PopED-0.1.2/PopED/inst/examples/PopED_output_summary_D_cont_opt_1.txt |only
PopED-0.1.2/PopED/inst/examples/ex.1.a.PK.1.comp.oral.md.intro.R | 55 -
PopED-0.1.2/PopED/inst/examples/ex.1.b.PK.1.comp.oral.md.re-parameterize.R | 39 +
PopED-0.1.2/PopED/inst/examples/ex.1.c.PK.1.comp.oral.md.ODE.R | 27
PopED-0.1.2/PopED/inst/examples/ex.2.a.warfarin.evaluate.R | 13
PopED-0.1.2/PopED/inst/examples/ex.2.b.warfarin.optimize.R | 60 +-
PopED-0.1.2/PopED/inst/examples/ex.2.c.warfarin.discrete.optimization.R | 35 +
PopED-0.1.2/PopED/inst/examples/ex.2.d.warfarin.ODE.compiled.R |only
PopED-0.1.2/PopED/inst/examples/ex.2.e.warfarin.ED.R | 40 +
PopED-0.1.2/PopED/inst/examples/ex.2.f.warfarin.Ds.R | 23
PopED-0.1.2/PopED/inst/examples/ex.3.a.PKPD.1.comp.oral.md.imax.D-opt.R | 17
PopED-0.1.2/PopED/inst/examples/ex.3.b.PKPD.1.comp.oral.md.imax.ED-opt.R | 34 -
PopED-0.1.2/PopED/inst/examples/ex.4.PKPD.1.comp.emax.R | 26
PopED-0.1.2/PopED/inst/examples/ex.5.PD.emax.hill.R | 25
PopED-0.1.2/PopED/inst/examples/ex.6.PK.1.comp.oral.sd.R | 65 +-
PopED-0.1.2/PopED/inst/examples/ex.7.PK.1.comp.maturation.R | 44 +
PopED-0.1.2/PopED/inst/examples/ex.8.a.tmdd_qss_one_target.R |only
PopED-0.1.2/PopED/inst/examples/ex.8.b.tmdd_qss_one_target_compiled.R |only
PopED-0.1.2/PopED/inst/examples/ex.9.PK.2.comp.oral.md.ode.compiled.R |only
PopED-0.1.2/PopED/inst/examples/one_comp_oral_CL.c |only
PopED-0.1.2/PopED/inst/examples/test.csv |only
PopED-0.1.2/PopED/inst/examples/tmdd_qss_one_target.c |only
PopED-0.1.2/PopED/inst/examples/two_comp_oral_CL.c |only
PopED-0.1.2/PopED/inst/shinyapp/server.R | 167 +++---
PopED-0.1.2/PopED/inst/shinyapp/ui.R | 8
PopED-0.1.2/PopED/man/Doptim.Rd | 54 +
PopED-0.1.2/PopED/man/Dtrace.Rd | 12
PopED-0.1.2/PopED/man/LEDoptim.Rd | 70 +-
PopED-0.1.2/PopED/man/LinMatrixH.Rd | 14
PopED-0.1.2/PopED/man/LinMatrixL.Rd | 18
PopED-0.1.2/PopED/man/LinMatrixLH.Rd | 14
PopED-0.1.2/PopED/man/LinMatrixL_occ.Rd | 14
PopED-0.1.2/PopED/man/PopED-internal.Rd | 1
PopED-0.1.2/PopED/man/PopED-package.Rd | 2
PopED-0.1.2/PopED/man/RS_opt.Rd | 60 +-
PopED-0.1.2/PopED/man/RS_opt_gen.Rd | 80 +-
PopED-0.1.2/PopED/man/a_line_search.Rd | 14
PopED-0.1.2/PopED/man/bfgsb_min.Rd | 2
PopED-0.1.2/PopED/man/blockexp.Rd | 6
PopED-0.1.2/PopED/man/blockfinal.Rd | 42 -
PopED-0.1.2/PopED/man/blockheader.Rd | 36 -
PopED-0.1.2/PopED/man/blockopt.Rd | 6
PopED-0.1.2/PopED/man/calc_autofocus.Rd | 22
PopED-0.1.2/PopED/man/calc_ofv_and_fim.Rd | 62 +-
PopED-0.1.2/PopED/man/calc_ofv_and_grad.Rd | 30 -
PopED-0.1.2/PopED/man/cell.Rd | 2
PopED-0.1.2/PopED/man/convert_variables.Rd | 40 -
PopED-0.1.2/PopED/man/create.poped.database.Rd | 88 +--
PopED-0.1.2/PopED/man/create_design.Rd |only
PopED-0.1.2/PopED/man/create_design_space.Rd |only
PopED-0.1.2/PopED/man/diag_matlab.Rd | 2
PopED-0.1.2/PopED/man/downsizing_general_design.Rd | 5
PopED-0.1.2/PopED/man/ed_laplace_ofv.Rd | 52 -
PopED-0.1.2/PopED/man/ed_mftot.Rd | 16
PopED-0.1.2/PopED/man/evaluate.e.ofv.fim.Rd | 56 +-
PopED-0.1.2/PopED/man/evaluate.fim.Rd | 2
PopED-0.1.2/PopED/man/feps.add.Rd | 8
PopED-0.1.2/PopED/man/feps.add.prop.Rd | 8
PopED-0.1.2/PopED/man/feps.prop.Rd | 8
PopED-0.1.2/PopED/man/feval.Rd | 4
PopED-0.1.2/PopED/man/ff.PK.1.comp.oral.md.CL.Rd | 2
PopED-0.1.2/PopED/man/ff.PK.1.comp.oral.md.KE.Rd | 2
PopED-0.1.2/PopED/man/ff.PK.1.comp.oral.sd.CL.Rd | 2
PopED-0.1.2/PopED/man/ff.PK.1.comp.oral.sd.KE.Rd | 2
PopED-0.1.2/PopED/man/ff.PKPD.1.comp.oral.md.CL.imax.Rd | 2
PopED-0.1.2/PopED/man/ff.PKPD.1.comp.sd.CL.emax.Rd | 2
PopED-0.1.2/PopED/man/fileparts.Rd | 2
PopED-0.1.2/PopED/man/getTruncatedNormal.Rd | 2
PopED-0.1.2/PopED/man/get_all_params.Rd | 2
PopED-0.1.2/PopED/man/get_rse.Rd | 38 -
PopED-0.1.2/PopED/man/getfulld.Rd | 4
PopED-0.1.2/PopED/man/gradf_eps.Rd | 14
PopED-0.1.2/PopED/man/isempty.Rd | 2
PopED-0.1.2/PopED/man/isfield.Rd | 2
PopED-0.1.2/PopED/man/log_prior_pdf.Rd | 6
PopED-0.1.2/PopED/man/mf.Rd | 6
PopED-0.1.2/PopED/man/mf3.Rd | 6
PopED-0.1.2/PopED/man/mf5.Rd | 2
PopED-0.1.2/PopED/man/mf6.Rd | 2
PopED-0.1.2/PopED/man/mf7.Rd | 2
PopED-0.1.2/PopED/man/mf8.Rd | 2
PopED-0.1.2/PopED/man/mfea.Rd | 10
PopED-0.1.2/PopED/man/mftot.Rd | 24
PopED-0.1.2/PopED/man/mftot0.Rd | 2
PopED-0.1.2/PopED/man/mftot1.Rd | 2
PopED-0.1.2/PopED/man/mftot2.Rd | 2
PopED-0.1.2/PopED/man/mftot3.Rd | 2
PopED-0.1.2/PopED/man/mftot4.Rd | 2
PopED-0.1.2/PopED/man/mftot5.Rd | 2
PopED-0.1.2/PopED/man/mftot6.Rd | 2
PopED-0.1.2/PopED/man/mftot7.Rd | 2
PopED-0.1.2/PopED/man/model_prediction.Rd | 172 +++++-
PopED-0.1.2/PopED/man/ofv_criterion.Rd | 2
PopED-0.1.2/PopED/man/ofv_fim.Rd | 6
PopED-0.1.2/PopED/man/ones.Rd | 2
PopED-0.1.2/PopED/man/pargen.Rd | 2
PopED-0.1.2/PopED/man/plot_efficiency_of_windows.Rd | 48 +
PopED-0.1.2/PopED/man/plot_model_prediction.Rd | 31 -
PopED-0.1.2/PopED/man/poped.choose.Rd | 4
PopED-0.1.2/PopED/man/poped_optimize.Rd | 46 -
PopED-0.1.2/PopED/man/rand.Rd | 2
PopED-0.1.2/PopED/man/randn.Rd | 2
PopED-0.1.2/PopED/man/randperm.Rd | 2
PopED-0.1.2/PopED/man/size.Rd | 2
PopED-0.1.2/PopED/man/test_for_max.Rd | 2
PopED-0.1.2/PopED/man/test_for_min.Rd | 2
PopED-0.1.2/PopED/man/test_for_zeros.Rd | 2
PopED-0.1.2/PopED/man/test_mat_size.Rd | 2
PopED-0.1.2/PopED/man/tic.Rd | 2
PopED-0.1.2/PopED/man/toc.Rd | 2
PopED-0.1.2/PopED/man/zeros.Rd | 2
PopED-0.1.2/PopED/tests/testthat/PopED_output_summary_D_cont_opt_1.txt |only
PopED-0.1.2/PopED/tests/testthat/PopED_output_summary_ED_Laplace_opt.txt |only
PopED-0.1.2/PopED/tests/testthat/PopED_output_summary_RS_1.txt |only
PopED-0.1.2/PopED/tests/testthat/PopED_output_summary_mfea_opt_1.txt |only
PopED-0.1.2/PopED/tests/testthat/Rplots.pdf |only
PopED-0.1.2/PopED/tests/testthat/examples_fcn_doc/examples_create_design.R |only
PopED-0.1.2/PopED/tests/testthat/examples_fcn_doc/examples_create_design_space.R |only
PopED-0.1.2/PopED/tests/testthat/examples_fcn_doc/examples_model_prediction.R | 99 +++
PopED-0.1.2/PopED/tests/testthat/examples_fcn_doc/examples_plot_efficiency_of_windows.R | 20
PopED-0.1.2/PopED/tests/testthat/test_create_databases.R |only
PopED-0.1.2/PopED/tests/testthat/test_examples.R |only
PopED-0.1.2/PopED/tests/testthat/test_predictions.R |only
149 files changed, 1929 insertions(+), 1577 deletions(-)
Title: R tools for making it easier to combine and clean data sets.
Diff between DataCombine versions 0.2.2 dated 2014-08-13 and 0.2.7 dated 2014-11-19
Description: R tools for combining and cleaning data sets, including filling in
missing observations with data from another data frame and creating
lag/lead variables.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
DESCRIPTION | 8 +-
MD5 | 55 +++++++--------
NAMESPACE | 4 -
NEWS | 28 +++++++
R/FillIn.R | 189 ++++++++++++++++++++++++++++++++---------------------
R/TimeFill.R | 4 -
R/slide.R | 91 +++++++++++++++++++------
R/utils.R | 93 +++++++++++++-------------
README.md | 65 ++++++++++++------
man/CountSpell.Rd | 4 -
man/DropNA.Rd | 2
man/FillDown.Rd |only
man/FillIn.Rd | 35 ++++++---
man/FindReplace.Rd | 2
man/InsertRow.Rd | 2
man/MoveFront.Rd | 2
man/NaVar.Rd | 2
man/PercChange.Rd | 2
man/SpreadDummy.Rd | 2
man/StartEnd.Rd | 2
man/TimeFill.Rd | 2
man/VarDrop.Rd | 2
man/dMerge.Rd | 2
man/grepl.sub.Rd | 2
man/rmExcept.Rd | 2
man/shift.Rd | 2
man/shiftMA.Rd | 2
man/slide.Rd | 30 +++++---
man/slideMA.Rd | 2
29 files changed, 408 insertions(+), 230 deletions(-)
Title: Recovering a Basic Space from Issue Scales
Diff between basicspace versions 0.13 dated 2014-11-09 and 0.15 dated 2014-11-19
Description: Conducts Aldrich-McKelvey and Blackbox Scaling to Recover
Latent Dimensions of Judgment
Author: Keith Poole
Maintainer: James Lo
ChangeLog | 2
DESCRIPTION | 8 +--
MD5 | 50 +++++++++++------------
data/Issues1980_bb.rda |only
man/Issues1980.Rd | 9 +++-
man/Issues1980_bb.Rd |only
man/LC1980_bbt.Rd | 11 +++--
man/blackbox.Rd | 10 +++-
man/blackbox_transpose.Rd | 6 +-
man/boot_aldmck.Rd | 4 +
man/boot_blackbt.Rd | 14 ++++--
man/bootbbt.Rd | 18 +++++---
man/colombia.Rd | 4 -
man/fit.Rd | 17 +++++--
man/individuals.Rd | 8 ++-
man/plot.blackbox.Rd | 100 +++++++++++++++++++++++++++++-----------------
man/plot.blackbt.Rd | 5 ++
man/plot.boot_aldmck.Rd | 89 +++++++++++++++++++++++++---------------
man/plot.boot_blackbt.Rd | 89 +++++++++++++++++++++++++---------------
man/plot.cdf.Rd | 1
man/plotcdf.blackbt.Rd | 3 -
man/predict.blackbox.Rd | 12 +++--
man/stimuli.Rd | 8 ++-
man/summary.blackbox.Rd | 8 ++-
man/summary.blackbt.Rd | 6 +-
src/basicspace.f90 | 43 +++++--------------
vignettes/basicspace.Rnw | 25 +++++++----
27 files changed, 334 insertions(+), 216 deletions(-)
Title: PCIC Implementation of Climdex Routines
Diff between climdex.pcic versions 1.1-1 dated 2014-04-03 and 1.1-4 dated 2014-11-19
Description: PCIC's implementation of Climdex routines for computation of
extreme climate indices.
Author: David Bronaugh
Maintainer: James Hiebert
CHANGELOG | 11 +-
COPYING |only
DESCRIPTION | 21 ++--
MD5 | 103 ++++++++++----------
NAMESPACE | 2
R/climdex.pcic-package.R | 3
R/climdex.r | 3
man/climdex.cdd.Rd | 15 +-
man/climdex.csdi.Rd | 47 ++++-----
man/climdex.cwd.Rd | 15 +-
man/climdex.dtr.Rd | 20 +--
man/climdex.fd.Rd | 13 +-
man/climdex.get.available.indices.Rd | 18 +--
man/climdex.gsl.Rd | 66 +++++-------
man/climdex.id.Rd | 13 +-
man/climdex.pcic.Rd | 76 ++++++--------
man/climdex.prcptot.Rd | 16 +--
man/climdex.quantile.Rd | 12 +-
man/climdex.r10mm.Rd | 11 --
man/climdex.r20mm.Rd | 11 --
man/climdex.r95ptot.Rd | 15 +-
man/climdex.r99ptot.Rd | 15 +-
man/climdex.rnnmm.Rd | 14 +-
man/climdex.rx1day.Rd | 29 ++---
man/climdex.rx5day.Rd | 34 ++----
man/climdex.sdii.Rd | 19 +--
man/climdex.su.Rd | 16 +--
man/climdex.tn10p.Rd | 62 +++++-------
man/climdex.tn90p.Rd | 62 +++++-------
man/climdex.tnn.Rd | 13 +-
man/climdex.tnx.Rd | 13 +-
man/climdex.tr.Rd | 13 +-
man/climdex.tx10p.Rd | 62 +++++-------
man/climdex.tx90p.Rd | 62 +++++-------
man/climdex.txn.Rd | 13 +-
man/climdex.txx.Rd | 13 +-
man/climdex.wsdi.Rd | 47 ++++-----
man/climdexInput.Rd | 144 +++++++++++++---------------
man/climdexInput.csv.Rd | 132 ++++++++++---------------
man/climdexInput.raw.Rd | 60 ++++-------
man/ec.1018935.Rd | 20 +--
man/get.last.monthday.of.year.Rd | 12 +-
man/get.outofbase.quantiles.Rd | 57 ++++-------
man/get.series.lengths.at.ends.Rd | 21 +---
man/growing.season.length.Rd | 59 +++++------
man/nday.consec.prec.max.Rd | 30 ++---
man/number.days.op.threshold.Rd | 26 ++---
man/percent.days.op.threshold.Rd | 42 +++-----
man/select.blocks.gt.length.Rd | 24 ++--
man/simple.precipitation.intensity.index.Rd | 21 +---
man/spell.length.max.Rd | 33 ++----
man/threshold.exceedance.duration.index.Rd | 46 +++-----
man/total.precip.op.threshold.Rd | 21 +---
53 files changed, 784 insertions(+), 942 deletions(-)