Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-21 0.9-3
2011-05-24 0.9-2
2011-05-20 0.9-1
2011-05-19 0.9-0
2009-08-01 0.8-5
2008-11-02 0.8-4
2008-09-16 0.8-3
2007-12-24 0.8-2
2007-06-16 0.8-1
Title: Modelling Space Time AutoRegressive Moving Average (STARMA)
Processes
Description: Statistical functions to identify, estimate and diagnose a Space-Time AutoRegressive Moving Average (STARMA) model.
Author: Felix Cheysson
Maintainer: Felix Cheysson <felix@cheysson.fr>
Diff between starma versions 1.1 dated 2015-10-05 and 1.2 dated 2015-11-12
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- man/stacf.Rd | 2 +- man/starma-package.Rd | 6 +++--- man/stcor.test.Rd | 2 +- src/starma.cpp | 2 +- 6 files changed, 18 insertions(+), 17 deletions(-)
Title: Statistical Methods for Regional Counts
Description: Provides statistical methods for the analysis of data areal data, with a focus on cluster detection.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smerc versions 0.1.6 dated 2015-10-06 and 0.2.2 dated 2015-11-12
DESCRIPTION | 13 ++-- MD5 | 35 ++++++++--- NAMESPACE | 8 ++ R/flex.test.R |only R/flex.zones.R |only R/scan.stat.R | 18 +++-- R/scan.test.R | 125 +++++++++++++++++++++------------------- R/uls.test.R | 45 ++++---------- man/flex.test.Rd |only man/flex.zones.Rd |only man/scan.stat.Rd | 12 +-- man/scan.test.Rd | 5 - man/uls.test.Rd | 9 +- tests/flex_nycases.txt |only tests/flex_nycoords.txt |only tests/flex_nyw.mt0 |only tests/flex_nyw.txt |only tests/flex_out.ed$ |only tests/flex_out.fl$ |only tests/flex_out.la$ |only tests/flex_out.no$ |only tests/flex_out.txt |only tests/flex_out.txt.clt |only tests/flexscanformat.R |only tests/satscanformat.R |only tests/testthat/test-flex.test.R |only tests/testthat/test-scan.test.R | 3 27 files changed, 148 insertions(+), 125 deletions(-)
Title: Fast and Light-Weight Caching (Memoization) of Objects and
Results to Speed Up Computations
Description: Memoization can be used to speed up repetitive and computational expensive function calls. The first time a function that implements memoization is called the results are stored in a cache memory. The next time the function is called with the same set of parameters, the results are momentarily retrieved from the cache avoiding repeating the calculations. With this package, any R object can be cached in a key-value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.cache versions 0.10.0 dated 2014-06-11 and 0.12.0 dated 2015-11-12
DESCRIPTION | 20 ++++++++--------- MD5 | 49 +++++++++++++++++++++++++++----------------- NAMESPACE | 1 NEWS | 23 ++++++++++++++++++++ R/999.package.R | 20 ++++++----------- R/addMemoization.R | 24 +++++++++++++++++---- R/clearCache.R | 6 ++--- R/getChecksum.R | 2 - R/loadCache.R | 10 +------- R/memoizedCall.R | 24 +++++++++++++-------- R/private.assertDigest.R | 4 +-- R/readCacheHeader.R | 8 ++----- R/saveCache.R | 10 +------- R/zzz.R | 2 + README.md |only man/R.cache-package.Rd | 10 +------- man/addMemoization.Rd | 6 ++++- man/loadCache.Rd | 10 +------- man/memoizedCall.Rd | 9 +++++--- man/saveCache.Rd | 8 ------- tests/Object.getChecksum.R |only tests/addMemoization.R |only tests/clearCache.R |only tests/evalWithMemoization.R |only tests/getCachePath.R |only tests/getCacheRootPath.R |only tests/loadCache.R |only tests/memoizedCall.R |only tests/readCacheHeader.R |only tests/setCachePath.R |only tests/setCacheRootPath.R |only tests/textPrompt.R |only 32 files changed, 137 insertions(+), 109 deletions(-)
Title: Bayesian Variable Selection with Hierarchical Priors
Description:
Bayesian variable selection for linear regression models using hierarchical
priors. There is a prior that combines information across responses and one
that combines information across covariates, as well as a standard spike and
slab prior for comparison. An MCMC samples from the marginal posterior
distribution for the 0-1 variables indicating if each covariate belongs to the
model for each response.
Author: Laurel Stell and Chiara Sabatti
Maintainer: Laurel Stell <lstell@stanford.edu>
Diff between ptycho versions 1.1-2 dated 2015-09-12 and 1.1-4 dated 2015-11-12
ptycho-1.1-2/ptycho/man/data.Rd |only ptycho-1.1-2/ptycho/man/mcmcLoop.Rd |only ptycho-1.1-4/ptycho/DESCRIPTION | 9 +- ptycho-1.1-4/ptycho/MD5 | 17 ++--- ptycho-1.1-4/ptycho/NAMESPACE | 4 - ptycho-1.1-4/ptycho/R/batch.R | 65 ++++++++++--------- ptycho-1.1-4/ptycho/R/gendata.R | 39 ++++++++++- ptycho-1.1-4/ptycho/R/mh.R | 48 +++++++++----- ptycho-1.1-4/ptycho/man/Data.Rd |only ptycho-1.1-4/ptycho/man/createData.Rd | 17 +++-- ptycho-1.1-4/ptycho/man/ptycho.Rd | 112 ++++++++++++++++++++++------------ 11 files changed, 202 insertions(+), 109 deletions(-)
Title: Utilities to Fit Paired Comparison Models for Preferences
Description: Generates design matrix for analysing real paired comparisons and derived paired comparison data (Likert type items/ratings or rankings) using a loglinear approach. Fits loglinear Bradley-Terry model (LLBT) exploiting an eliminate feature. Computes pattern models for paired comparisons, rankings, and ratings. Some treatment of missing values (MCAR and MNAR). Fits latent class (mixture) models for paired comparison, rating and ranking patterns using a non-parametric ML approach.
Author: Reinhold Hatzinger [aut],
Marco Johannes Maier [cre]
Maintainer: Marco Johannes Maier <marco.maier@wu.ac.at>
Diff between prefmod versions 0.8-32 dated 2014-05-20 and 0.8-33 dated 2015-11-12
.Rinstignore |only DESCRIPTION | 17 ++-- MD5 | 42 +++++----- NAMESPACE | 55 +++++++------- R/plotworth.R | 188 +++++++++++++++++++++++++----------------------- build/partial.rdb |binary data/baseball.RData |binary data/carconf.RData |binary data/cemspc.RData |binary data/dat4.RData |binary data/euro55.2.des.RData |binary data/immig.RData |binary data/issp2000.RData |binary data/music.RData |binary data/salad.RData |binary data/tennis.RData |binary data/trdel.RData |binary data/xmpl.RData |binary inst/CITATION | 2 man/issp2000.Rd | 24 +++--- man/music.Rd | 3 man/plot.wmat.Rd | 6 + man/prefmod-package.Rd | 2 23 files changed, 184 insertions(+), 155 deletions(-)
Title: Fragment Analysis in R
Description: Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file and contains DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
Author: Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa.
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between Fragman versions 1.0.1 dated 2015-09-22 and 1.0.2 dated 2015-11-12
DESCRIPTION | 8 MD5 | 36 ++-- NAMESPACE | 7 R/find.ladder.R | 392 ++++++++++++++++++++++++++++++++++++++-------- R/jm.conv.R | 2 R/ladder.corrector.R |only R/ladder.info.attach.R | 36 +++- R/overview.R | 2 R/overview2.R | 8 R/pullup.R | 3 R/score.easy.R | 29 +-- R/storing.inds.R | 44 ++++- man/Fragman-package.Rd | 8 man/find.ladder.Rd | 6 man/ladder.corrector.Rd |only man/ladder.info.attach.Rd | 10 - man/overview.Rd | 4 man/overview2.Rd | 6 man/score.easy.Rd | 8 man/storing.inds.Rd | 6 20 files changed, 486 insertions(+), 129 deletions(-)
Title: Extended Rasch Modeling
Description: The eRm package fits Rasch models (RM), linear logistic test models (LLTM), rating scale model (RSM), linear rating scale models (LRSM), partial credit models (PCM), and linear partial credit models (LPCM). Missing values are allowed in the data matrix. Additional features are the ML estimation of the person parameters, Andersen's LR-test, item-specific Wald test, Martin-Löf-Test, nonparametric Monte-Carlo Tests, itemfit and personfit statistics including infit and outfit measures, various ICC and related plots, automated stepwise item elimination, simulation module for various binary data matrices. An eRm platform is provided at R-forge (see URL).
Author: Patrick Mair [cre, aut],
Reinhold Hatzinger [aut],
Marco J. Maier [aut],
Thomas Rusch [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between eRm versions 0.15-5 dated 2015-01-10 and 0.15-6 dated 2015-11-12
DESCRIPTION | 13 ++++---- MD5 | 62 ++++++++++++++++++++-------------------- NAMESPACE | 2 - NEWS | 8 +++++ R/plotGOF.LR.R | 36 ++++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary data/llraDat1.rda |binary data/llraDat2.rda |binary data/llradat3.rda |binary data/lltmdat1.rda |binary data/lltmdat2.rda |binary data/lpcmdat.rda |binary data/lrsmdat.rda |binary data/pcmdat.rda |binary data/pcmdat2.rda |binary data/raschdat1.rda |binary data/raschdat1_RM_fitted.RData |binary data/raschdat1_RM_lrres2.RData |binary data/raschdat1_RM_plotDIF.RData |binary data/raschdat2.rda |binary data/raschdat3.rda |binary data/raschdat4.rda |binary data/rsmdat.rda |binary data/xmpl.RData |binary data/xmplbig.RData |binary inst/CITATION | 8 ++--- inst/NEWS.Rd | 6 +++ inst/NEWS.pdf |binary inst/doc/eRm.pdf |binary man/LRtest.Rd | 26 ++++++++++++++-- man/NPtest.Rd | 2 - 32 files changed, 100 insertions(+), 63 deletions(-)
Title: Dirichlet Regression in R
Description: Implements Dirichlet regression models in R.
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier <marco.maier@wu.ac.at>
Diff between DirichletReg versions 0.6-2 dated 2015-02-09 and 0.6-3 dated 2015-11-12
DirichletReg-0.6-2/DirichletReg/R/lines.DirichletRegData.R |only DirichletReg-0.6-3/DirichletReg/DESCRIPTION | 8 - DirichletReg-0.6-3/DirichletReg/MD5 | 67 ++++---- DirichletReg-0.6-3/DirichletReg/NAMESPACE | 2 DirichletReg-0.6-3/DirichletReg/NEWS | 2 DirichletReg-0.6-3/DirichletReg/R/DR_LL_alt.R | 44 ++--- DirichletReg-0.6-3/DirichletReg/R/DR_LL_common.R | 28 +-- DirichletReg-0.6-3/DirichletReg/R/DR_data.R | 38 ++-- DirichletReg-0.6-3/DirichletReg/R/DirichReg.R | 78 +++++----- DirichletReg-0.6-3/DirichletReg/R/DirichReg_fit.R | 28 +-- DirichletReg-0.6-3/DirichletReg/R/Dirichlet.R | 36 ++-- DirichletReg-0.6-3/DirichletReg/R/confint.DirichletRegModel.R | 2 DirichletReg-0.6-3/DirichletReg/R/drop1.DirichletRegModel.R | 28 +-- DirichletReg-0.6-3/DirichletReg/R/get_starting_values.R | 12 - DirichletReg-0.6-3/DirichletReg/R/make.VT.R | 16 +- DirichletReg-0.6-3/DirichletReg/R/plot.DirichletRegData.R | 20 +- DirichletReg-0.6-3/DirichletReg/R/plot.DirichletRegModel.R | 8 - DirichletReg-0.6-3/DirichletReg/R/plot_DRdata_3d.R | 22 +- DirichletReg-0.6-3/DirichletReg/R/plot_DRdata_4d.R | 22 +- DirichletReg-0.6-3/DirichletReg/R/predict.DirichletRegModel.R | 10 - DirichletReg-0.6-3/DirichletReg/R/residuals.DirichletRegModel.R | 8 - DirichletReg-0.6-3/DirichletReg/R/summary.DirichletRegModel.R | 12 - DirichletReg-0.6-3/DirichletReg/R/sysdata.rda |binary DirichletReg-0.6-3/DirichletReg/R/toTernaryQuaternary.R | 10 - DirichletReg-0.6-3/DirichletReg/R/zzz.R | 12 - DirichletReg-0.6-3/DirichletReg/build/partial.rdb |binary DirichletReg-0.6-3/DirichletReg/build/vignette.rds |binary DirichletReg-0.6-3/DirichletReg/data/ArcticLake.RData |binary DirichletReg-0.6-3/DirichletReg/data/BloodSamples.RData |binary DirichletReg-0.6-3/DirichletReg/data/GlacialTills.RData |binary DirichletReg-0.6-3/DirichletReg/data/ReadingSkills.RData |binary DirichletReg-0.6-3/DirichletReg/data/Rocks.RData |binary DirichletReg-0.6-3/DirichletReg/inst/NEWS.Rd | 1 DirichletReg-0.6-3/DirichletReg/inst/NEWS.pdf |binary DirichletReg-0.6-3/DirichletReg/inst/doc/DirichletReg-vig.pdf |binary 35 files changed, 258 insertions(+), 256 deletions(-)
Title: Bayesian Model Averaging using Bayesian Adaptive Sampling
Description: Package for Bayesian Model Averaging in linear models and
generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
Liang et al hyper-g priors (JASA 2008) or mixtures of
g-priors in GLMS of Li and Clyde 2015. Other model
selection criteria include AIC and BIC. Sampling
probabilities may be updated based on the sampled models
using Sampling w/out Replacement or an MCMC algorithm
samples models using the BAS tree structure as an efficient
hash table. Allows uniform or beta-binomial prior distributions on
models, and may force variables to always be included.
Author: Merlise Clyde [aut, cre, cph],
Michael Littman [ctb],
Quanli Wang [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb]
Maintainer: Merlise Clyde <clyde@stat.duke.edu>
Diff between BAS versions 1.0.6 dated 2015-10-27 and 1.0.8 dated 2015-11-12
CHANGELOG | 11 +++++ DESCRIPTION | 8 +-- MD5 | 39 ++++++++++------- R/bas.R | 4 - R/bas.gglm.R | 84 ++++++++++++++++++++++++++++++++++---- R/betapriors.R | 42 +++++++++++++++++++ R/cch.R |only R/hypergeometric1F1.R | 3 - man/hyper-g-n.Rd |only man/hyper2d.Rd |only man/hypergeometric1F1.Rd | 8 +-- man/intrinsic.Rd |only man/jeffreys.Rd |only man/tcchpriors.Rd |only src/ZS.approx.null.np.c | 19 ++++---- src/bayesreg.c | 66 ++++++++++++++++++++---------- src/betapriorfamily.c | 102 ++++++++++++++++++++++++++++++++++++++++++----- src/betapriorfamily.h | 6 ++ src/cch.c |only src/family.c | 4 - src/hg.approx.null.np.c | 20 +++++---- src/hyperg.c | 2 src/hypergeometric1F1.c | 5 +- src/sampleworep.c | 27 ++++++++---- 24 files changed, 350 insertions(+), 100 deletions(-)
Title: Tools for Mapping Multiple Complex Traits
Description: Provides tools for joint analysis of multiple traits in a backcross (BC) or recombinant inbred lines (RIL) population. It can be used to select an optimal subset of traits for multiple-trait mapping, analyze multiple traits via the SURE model, which can associate different QTL with different traits, and perform multiple-trait composite multiple-interval mapping.
Author: Riyan Cheng <riyan.cheng@anu.edu.au>
Maintainer: Riyan Cheng <riyan.cheng@anu.edu.au>
Diff between qtlmt versions 0.1-3 dated 2013-03-12 and 0.1-4 dated 2015-11-12
ChangeLog | 9 +++++-- DESCRIPTION | 18 ++++---------- MD5 | 24 +++++++++---------- NAMESPACE | 3 ++ R/mstep.R | 40 +++++++++++++++++++-------------- R/mtcmim.R | 40 +++++++++++++++------------------ R/sure.R | 65 ++++++++++++++++++++++++++++++++---------------------- data/etrait.RData |binary man/mtcmim.Rd | 16 ++++++------- man/mtcmimStep.Rd | 18 +++++++------- man/sureEps.Rd | 8 +++--- man/sureEst.Rd | 15 ++++++------ man/sureStep.Rd | 18 +++++++------- 13 files changed, 148 insertions(+), 126 deletions(-)
Title: Non-Parametric Trend Tests and Change-Point Detection
Description: The analysis of environmental data often requires
the detection of trends and change-points.
This package provides the Mann-Kendall Trend Test,
seasonal Mann-Kendall Test,
correlated seasonal Mann-Kendall Test,
partial Mann-Kendall Trend test,
(Seasonal) Sen's slope, partial correlation trend test and
change-point test after Pettitt.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between trend versions 0.0.1 dated 2015-03-24 and 0.0.2 dated 2015-11-12
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NAMESPACE | 10 +++++++++- inst/NEWS.Rd |only inst/doc/trend.pdf |binary man/trend-package.Rd | 10 +++++++--- 6 files changed, 25 insertions(+), 12 deletions(-)
Title: Analyze Shot Group Data
Description: Analyzes shooting data with respect to group shape,
precision, and accuracy. This includes graphical methods,
descriptive statistics, and inference tests using standard,
but also non-parametric and robust statistical methods.
Implements distributions for radial error in bivariate normal
variables. Works with files exported by OnTarget PC/TDS or
Taran, as well as with custom data files in text format.
Author: Daniel Wollschlaeger
Maintainer: Daniel Wollschlaeger <dwoll@kuci.org>
Diff between shotGroups versions 0.6.1 dated 2015-09-07 and 0.6.2 dated 2015-11-12
DESCRIPTION | 10 ++--- MD5 | 58 ++++++++++++++--------------- R/compareGroups.R | 7 ++- R/getCEP.R | 89 +++++++++++++++++++++++++++++++++++++--------- R/getHitProb.R | 9 +++- R/groupShape.R | 24 ++++++------ R/groupSpread.R | 41 ++++++++++++++------- R/hoyt.R | 6 +-- R/maxwell.R | 2 - R/mvnEll.R | 8 ++-- R/rayleigh.R | 2 - R/simRingCount.R | 2 - build/vignette.rds |binary data/DF300BLK.rda |binary data/DF300BLKhl.rda |binary data/DFcciHV.rda |binary data/DFcm.rda |binary data/DFinch.rda |binary data/DFlistCm.rda |binary data/DFsavage.rda |binary data/DFscar17.rda |binary data/DFtalon.rda |binary data/targets.rda |binary inst/ChangeLog | 9 ++++ inst/doc/shotGroups.Rnw | 5 +- inst/doc/shotGroups.pdf |binary man/getCEP.Rd | 3 + man/shotGroups-package.Rd | 6 +-- vignettes/lit.bib | 48 ++++++++++++++---------- vignettes/shotGroups.Rnw | 5 +- 30 files changed, 216 insertions(+), 118 deletions(-)
Title: Tabular Reporting Functions
Description: Provides tabular reporting functionalities to work with 'ReporteRs'
package: 'as.FlexTable' methods are available for 'ftable' and 'xtable' objects,
function 'FlexPivot' is producing a pivot table and 'freqtable' a percentage table,
a 'knitr' print method and a 'shiny' render function are provided for 'FlexTable' objects.
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@lysis-consultants.fr>
Diff between rtable versions 0.1.0 dated 2015-03-24 and 0.1.5 dated 2015-11-12
DESCRIPTION | 19 ++-- MD5 | 26 +++-- NAMESPACE | 11 ++ NEWS |only R/FlexPivot.R | 194 +++++++++++++++++++++++--------------------- R/FlexTable_coef.R |only R/FlexTable_quality.R |only R/freqtable.R | 2 R/get_color_dataset.R |only man/FlexPivot.Rd | 11 +- man/FlexTable_coef.Rd |only man/FlexTable_quality.Rd |only man/as.FlexTable.ftable.Rd | 2 man/as.FlexTable.xtable.Rd | 2 man/freqtable.Rd | 2 man/knit_print.FlexTable.Rd | 2 man/renderFlexTable.Rd | 2 17 files changed, 152 insertions(+), 121 deletions(-)
Title: Correlation and Regression Analyses for Randomized Response Data
Description: Univariate and multivariate methods to analyze
randomized response (RR) survey designs (e.g., Warner, S. L. (1965).
Randomized response: A survey technique for eliminating evasive answer
bias. Journal of the American Statistical Association, 60, 63–69).
Besides univariate estimates of true proportions, RR variables can be used
for correlations, as dependent variable in a logistic regression (with or
without random effects), as predictors in a linear regression, or as
dependent variable in a beta-binomial ANOVA. For simulation and bootstrap
purposes, RR data can be generated according to several models.
Author: Daniel W. Heck [aut, cre], Morten Moshagen [aut]
Maintainer: Daniel W. Heck <dheck@mail.uni-mannheim.de>
Diff between RRreg versions 0.4.1 dated 2015-07-28 and 0.5.0 dated 2015-11-12
RRreg-0.4.1/RRreg/R/RRlog.CDM.R |only RRreg-0.4.1/RRreg/R/RRlog.FR.R |only RRreg-0.4.1/RRreg/R/RRlog.Kuk.R |only RRreg-0.4.1/RRreg/R/RRlog.Mangat.R |only RRreg-0.4.1/RRreg/R/RRlog.SLD.R |only RRreg-0.4.1/RRreg/R/RRlog.UQTknown.R |only RRreg-0.4.1/RRreg/R/RRlog.UQTunknown.R |only RRreg-0.4.1/RRreg/R/RRlog.Warner.R |only RRreg-0.5.0/RRreg/DESCRIPTION | 19 +- RRreg-0.5.0/RRreg/MD5 | 66 +++---- RRreg-0.5.0/RRreg/NAMESPACE | 3 RRreg-0.5.0/RRreg/NEWS | 10 + RRreg-0.5.0/RRreg/R/RRanova.R |only RRreg-0.5.0/RRreg/R/RRcheck.R | 114 +++++++----- RRreg-0.5.0/RRreg/R/RRgen.R | 86 +++++---- RRreg-0.5.0/RRreg/R/RRlin.R | 6 RRreg-0.5.0/RRreg/R/RRlin.getPW.R | 45 +++- RRreg-0.5.0/RRreg/R/RRlog.R | 200 +++++++++++----------- RRreg-0.5.0/RRreg/R/RRlog_fit.R |only RRreg-0.5.0/RRreg/R/RRmixed.R |only RRreg-0.5.0/RRreg/R/RRreg-package.R | 32 ++- RRreg-0.5.0/RRreg/R/RRsimu.R | 20 +- RRreg-0.5.0/RRreg/R/RRuni.R | 143 ++++++++++----- RRreg-0.5.0/RRreg/R/RRuni.models.R | 21 +- RRreg-0.5.0/RRreg/R/RRuni_ll.R |only RRreg-0.5.0/RRreg/R/helper_functions.R | 25 ++ RRreg-0.5.0/RRreg/R/powerplot.R | 7 RRreg-0.5.0/RRreg/data |only RRreg-0.5.0/RRreg/inst/doc/RRreg.R | 9 RRreg-0.5.0/RRreg/inst/doc/RRreg.Rmd | 107 ++++++++--- RRreg-0.5.0/RRreg/inst/doc/RRreg.html | 262 +++++++++++++++++------------ RRreg-0.5.0/RRreg/inst/models |only RRreg-0.5.0/RRreg/man/RRgen.Rd | 8 RRreg-0.5.0/RRreg/man/RRlog.Rd | 16 + RRreg-0.5.0/RRreg/man/RRmixed.Rd |only RRreg-0.5.0/RRreg/man/RRreg-package.Rd | 10 - RRreg-0.5.0/RRreg/man/RRsimu.Rd | 4 RRreg-0.5.0/RRreg/man/RRuni.Rd | 47 ++--- RRreg-0.5.0/RRreg/man/getPW.Rd |only RRreg-0.5.0/RRreg/man/minarets.Rd |only RRreg-0.5.0/RRreg/vignettes/RRreg.Rmd | 107 ++++++++--- RRreg-0.5.0/RRreg/vignettes/markdown10.css | 6 42 files changed, 867 insertions(+), 506 deletions(-)
Title: Fast Network Modularity and Roles Computation by Simulated
Annealing (Rgraph C Library Wrapper for R)
Description: It provides functions to compute the modularity and modularity-related roles in networks. It is a wrapper around the rgraph library (Guimera & Amaral, 2005, doi:10.1038/nature03288).
Author: Guilhem Doulcier [aut, cre] (R bindings, current implementation of the
simulated annealing algorithm),
Roger Guimera [ctb] (Author of the original rgraph library),
Daniel B. Stouffer [aut, ths]
Maintainer: Guilhem Doulcier <guilhem.doulcier@ens.fr>
Diff between rnetcarto versions 0.2.3 dated 2015-11-11 and 0.2.4 dated 2015-11-12
DESCRIPTION | 8 ++--- MD5 | 6 ++-- inst/doc/getting-started.html | 55 +++++++++++++++++++--------------------- src/rgraph/src/fillpartitions.c | 41 ++++++++++------------------- 4 files changed, 49 insertions(+), 61 deletions(-)
Title: Random Effects Latent Class Analysis
Description: Fits standard and random effects latent class models. The single level random effects model is described in Qu et al (doi: 10.2307/2533043) and the two level random effects model in Beath and Heller (doi: 10.1177/1471082X0800900302). Examples are given for their use in diagnostic testing.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between randomLCA versions 1.0-3 dated 2015-09-30 and 1.0-5 dated 2015-11-12
randomLCA-1.0-3/randomLCA/vignettes/randomLCA-example.tex |only randomLCA-1.0-5/randomLCA/DESCRIPTION | 16 randomLCA-1.0-5/randomLCA/MD5 | 25 randomLCA-1.0-5/randomLCA/NAMESPACE | 94 +- randomLCA-1.0-5/randomLCA/R/fitAdaptRandom.R | 555 ++++++-------- randomLCA-1.0-5/randomLCA/R/outcomeProbs.R | 4 randomLCA-1.0-5/randomLCA/R/randomLCA.R | 342 ++++---- randomLCA-1.0-5/randomLCA/R/refit.randomLCA.R | 90 +- randomLCA-1.0-5/randomLCA/build/vignette.rds |binary randomLCA-1.0-5/randomLCA/inst/NEWS | 14 randomLCA-1.0-5/randomLCA/man/plot.Rd | 72 - randomLCA-1.0-5/randomLCA/man/refit.Rd | 8 randomLCA-1.0-5/randomLCA/man/simulate.Rd | 27 randomLCA-1.0-5/randomLCA/man/uterinecarcinoma.Rd | 6 14 files changed, 644 insertions(+), 609 deletions(-)
Title: Permutations and Mallows Distributions
Description: Includes functions to work with the Mallows and Generalized Mallows Models. The considered distances are Kendall's-tau, Cayley, Hamming and Ulam and it includes functions for making inference, sampling and learning such distributions, some of which are novel in the literature. As a by-product, PerMallows also includes operations for permutations, paying special attention to those related with the Kendall's-tau, Cayley, Ulam and Hamming distances. It is also possible to generate random permutations at a given distance, or with a given number of inversions, or cycles, or fixed points or even with a given length on LIS (longest increasing subsequence).
Author: Ekhine Irurozki <ekhine.irurozqui@ehu.eus>, Borja Calvo <borja.calvo@ehu.eus>, Jose A. Lozano <ja.lozano@ehu.eus>
Maintainer: Ekhine Irurozki <ekhine.irurozqui@ehu.eus>
Diff between PerMallows versions 1.8 dated 2015-01-27 and 1.10 dated 2015-11-12
PerMallows-1.10/PerMallows/DESCRIPTION | 15 PerMallows-1.10/PerMallows/MD5 | 92 PerMallows-1.10/PerMallows/NAMESPACE | 1 PerMallows-1.10/PerMallows/R/PerMallows.R | 441 +--- PerMallows-1.10/PerMallows/man/compose.Rd | 2 PerMallows-1.10/PerMallows/man/count.perms.Rd |only PerMallows-1.10/PerMallows/man/cycle2str.Rd | 4 PerMallows-1.10/PerMallows/man/cycles2perm.Rd |only PerMallows-1.10/PerMallows/man/data.apa.Rd | 2 PerMallows-1.10/PerMallows/man/data.order.Rd | 2 PerMallows-1.10/PerMallows/man/decomp2perm.Rd |only PerMallows-1.10/PerMallows/man/dgmm.Rd | 6 PerMallows-1.10/PerMallows/man/distance.Rd | 2 PerMallows-1.10/PerMallows/man/dmm.Rd | 6 PerMallows-1.10/PerMallows/man/expectation.gmm.Rd | 2 PerMallows-1.10/PerMallows/man/expectation.mm.Rd | 2 PerMallows-1.10/PerMallows/man/freq.matrix.Rd | 2 PerMallows-1.10/PerMallows/man/generate.aux.files.Rd | 2 PerMallows-1.10/PerMallows/man/identity.permutation.Rd | 2 PerMallows-1.10/PerMallows/man/insert.Rd |only PerMallows-1.10/PerMallows/man/inverse.perm.Rd |only PerMallows-1.10/PerMallows/man/inversion.Rd |only PerMallows-1.10/PerMallows/man/is.permutation.Rd | 4 PerMallows-1.10/PerMallows/man/lgmm.Rd | 16 PerMallows-1.10/PerMallows/man/lgmm.theta.Rd | 16 PerMallows-1.10/PerMallows/man/lmm.Rd | 18 PerMallows-1.10/PerMallows/man/lmm.theta.Rd | 18 PerMallows-1.10/PerMallows/man/marginal.Rd | 2 PerMallows-1.10/PerMallows/man/maxi.dist.Rd | 2 PerMallows-1.10/PerMallows/man/order.ratings.Rd | 2 PerMallows-1.10/PerMallows/man/perm.sample.med.Rd | 2 PerMallows-1.10/PerMallows/man/perm.sample.small.Rd | 2 PerMallows-1.10/PerMallows/man/perm2cycles.Rd |only PerMallows-1.10/PerMallows/man/perm2decomp.Rd |only PerMallows-1.10/PerMallows/man/permutations.of.Rd | 2 PerMallows-1.10/PerMallows/man/rdist.Rd |only PerMallows-1.10/PerMallows/man/read.perms.Rd |only PerMallows-1.10/PerMallows/man/rgmm.Rd | 5 PerMallows-1.10/PerMallows/man/rmm.Rd | 8 PerMallows-1.10/PerMallows/man/runif.permutation.Rd | 2 PerMallows-1.10/PerMallows/man/swap.Rd | 2 PerMallows-1.10/PerMallows/src/Cayley.cpp | 71 PerMallows-1.10/PerMallows/src/Cayley.h | 6 PerMallows-1.10/PerMallows/vignettes/PerMallows.tex | 1066 +++++----- PerMallows-1.8/PerMallows/man/count.derangements.Rd |only PerMallows-1.8/PerMallows/man/count.perms.cycles.Rd |only PerMallows-1.8/PerMallows/man/count.perms.distance.Rd |only PerMallows-1.8/PerMallows/man/count.perms.fixed.points.Rd |only PerMallows-1.8/PerMallows/man/count.perms.unfixed.points.gtet.Rd |only PerMallows-1.8/PerMallows/man/cycles2permutation.Rd |only PerMallows-1.8/PerMallows/man/decomposition2permutation.Rd |only PerMallows-1.8/PerMallows/man/insert.at.Rd |only PerMallows-1.8/PerMallows/man/inverse.permutation.Rd |only PerMallows-1.8/PerMallows/man/inversion.at.Rd |only PerMallows-1.8/PerMallows/man/permutation2cycles.Rd |only PerMallows-1.8/PerMallows/man/permutation2decomposition.Rd |only PerMallows-1.8/PerMallows/man/r.derangement.Rd |only PerMallows-1.8/PerMallows/man/r.dist.d.Rd |only PerMallows-1.8/PerMallows/man/r.perms.cycles.Rd |only PerMallows-1.8/PerMallows/man/read.permutation.file.Rd |only 60 files changed, 936 insertions(+), 891 deletions(-)
Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in
the Global Charcoal Database. Main functionalities includes data extraction
and sites selection, transformation and interpolation of the charcoal
records as well as compositing.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>
Diff between paleofire versions 1.1.6 dated 2015-04-22 and 1.1.7 dated 2015-11-12
DESCRIPTION | 8 +-- MD5 | 92 +++++++++++++++++++++---------------------- NAMESPACE | 20 +++++++-- NEWS | 12 +++++ R/pfCompositeLF.R | 2 R/pfGridding.R | 44 ++++++++++++-------- R/pfTransform.R | 36 ++++++++++++++-- build/vignette.rds |binary inst/CITATION | 2 inst/doc/paleofire-paper.pdf |binary man/checkGCDversion.Rd | 3 - man/contiguous.Rd | 3 - man/kdffreq.Rd | 3 - man/paleofire-internal.Rd | 3 - man/paleofire-package.Rd | 3 - man/pfAddData.Rd | 3 - man/pfBoxCox.Rd | 3 - man/pfCircular.Rd | 3 - man/pfComposite.Rd | 3 - man/pfCompositeLF.Rd | 11 ++--- man/pfDiagnostic.Rd | 9 ++-- man/pfDotMap.Rd | 13 +++--- man/pfExtract.Rd | 3 - man/pfGridding.Rd | 3 - man/pfInteractive.Rd | 3 - man/pfKruskal.Rd | 3 - man/pfMinMax.Rd | 3 - man/pfPublication.Rd | 3 - man/pfResolution.Rd | 3 - man/pfSimpleGrid.Rd | 3 - man/pfSiteSel.Rd | 3 - man/pfToKml.Rd | 3 - man/pfTransform.Rd | 9 ++-- man/plot.CHAR.Rd | 3 - man/plot.contiguous.Rd | 3 - man/plot.kdffreq.Rd | 7 +-- man/plot.pfCircular.Rd | 3 - man/plot.pfComposite.Rd | 7 +-- man/plot.pfCompositeLF.Rd | 3 - man/plot.pfGridding.Rd | 3 - man/plot.pfKruskal.Rd | 3 - man/plot.pfSiteSel.Rd | 3 - man/plot.potveg.Rd | 3 - man/potveg.Rd | 3 - man/pretreatment.Rd | 9 ++-- man/summary.pfSiteSel.Rd | 3 - man/triCube.Rd | 3 - 47 files changed, 233 insertions(+), 138 deletions(-)
Title: Methods for Multivariate Quadrature
Description: Provides methods to construct multivariate grids, which can be used
for multivariate quadrature. This grids can be based on different quadrature
rules like Newton-Cotes formulas (trapezoidal-, Simpson's- rule, ...) or Gauss
quadrature (Gauss-Hermite, Gauss-Legendre, ...). For the construction of the
multidimensional grid the product-rule or the combination- technique can be
applied.
Author: Constantin Weiser (HHU of Duesseldorf / Germany)
Maintainer: Constantin Weiser <weiserc@hhu.de>
Diff between mvQuad versions 1.0-3 dated 2015-11-03 and 1.0-4 dated 2015-11-12
DESCRIPTION | 22 +++++++++++----------- MD5 | 6 +++--- R/mvQuad.R | 23 ++++++++++++++--------- inst/NEWS | 7 ++++++- 4 files changed, 34 insertions(+), 24 deletions(-)
Title: Morse-Smale Approximation, Regression and Visualization
Description: Discrete Morse-Smale complex approximation based on kNN graph. The Morse-Smale complex provides a decomposition of the domain. This package provides methods to compute a hierarchical sequence of Morse-Smale complicies and tools that exploit this domain decomposition for regression and visualization of scalar functions.
Author: Samuel Gerber <sgerber@uoregon.edu>,
Kristi Potter <kpotter@sci.utah.edu>,
Oliver Ruebel <ruebel1@llnl.gov>
Maintainer: Samuel Gerber <sgerber@uoregon.edu>
Diff between msr versions 0.4.1 dated 2012-07-11 and 0.4.4 dated 2015-11-12
msr-0.4.1/msr/src/kd_dump.cpp |only msr-0.4.4/msr/ChangeLog | 6 msr-0.4.4/msr/DESCRIPTION | 29 msr-0.4.4/msr/MD5 | 61 - msr-0.4.4/msr/NAMESPACE | 16 msr-0.4.4/msr/data/camera_estimation.rda |binary msr-0.4.4/msr/data/diagonal.rda |binary msr-0.4.4/msr/data/fourpeaks.rda |binary msr-0.4.4/msr/data/uci_crime_subset.rda |binary msr-0.4.4/msr/man/msr-package.Rd | 9 msr-0.4.4/msr/src/ANN.cpp | 2 msr-0.4.4/msr/src/ANN/ANN.h | 6 msr-0.4.4/msr/src/DenseMatrix.h | 11 msr-0.4.4/msr/src/DenseVector.h | 12 msr-0.4.4/msr/src/EuclideanMetric.h | 16 msr-0.4.4/msr/src/GaussianKernel.h | 45 - msr-0.4.4/msr/src/Geometry.h | 31 msr-0.4.4/msr/src/Kernel.h | 14 msr-0.4.4/msr/src/KernelDensity.h | 14 msr-0.4.4/msr/src/LapackDefs.h |only msr-0.4.4/msr/src/Linalg.h | 984 +++++++++++++++-------------- msr-0.4.4/msr/src/LinalgIO.h | 5 msr-0.4.4/msr/src/Matrix.h | 3 msr-0.4.4/msr/src/Metric.h | 10 msr-0.4.4/msr/src/NNMSComplex.h | 99 +- msr-0.4.4/msr/src/NNMSComplex2old.h | 35 - msr-0.4.4/msr/src/SquaredEuclideanMetric.h |only msr-0.4.4/msr/src/Vector.h | 2 msr-0.4.4/msr/src/bd_tree.cpp | 2 msr-0.4.4/msr/src/bd_tree.h | 2 msr-0.4.4/msr/src/kd_tree.cpp | 7 msr-0.4.4/msr/src/kd_tree.h | 6 msr-0.4.4/msr/src/msr.cc | 9 33 files changed, 803 insertions(+), 633 deletions(-)
Title: Access and Process Data and Documents of the Manifesto Project
Description: Provides access to coded election programmes from
the Manifesto Corpus and to the Manifesto Project's Main Dataset and routines
to analyse this data. The Manifesto
Project (https://manifesto-project.wzb.eu) collects and analyses election
programmes across time and space to measure the political preferences
of parties. The Manifesto Corpus contains the collected
and annotated election programmes in the Corpus format of the package 'tm' to enable
easy use of text processing and text mining functionality. Specific functions
for scaling of coded political texts are included.
Author: Jirka Lewandowski [aut, cre],
Nicolas Merz [aut],
Sven Regel [ctb],
Pola Lehmann [ctb]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between manifestoR versions 1.0-5 dated 2015-09-14 and 1.1-1 dated 2015-11-12
ChangeLog | 12 ++ DESCRIPTION | 21 ++-- MD5 | 39 +++++---- NAMESPACE | 10 ++ R/codes.R | 169 +++++++++++++++++++++++++++++++++++---- R/corpus.R | 49 +++++++++-- R/db_api.R | 30 ++++-- R/globals.R | 11 +- R/issue_attention.R |only R/manifesto.R | 53 ++---------- R/manifestoR-package.r | 11 +- R/nicheness.R |only R/pipe_helpers.R |only R/scaling_rile.R | 25 ++++- build/vignette.rds |binary man/ManifestoCorpus.Rd | 4 man/ManifestoSource.Rd | 6 + man/aggregate_pers.Rd |only man/categories.Rd |only man/count_codes.Rd | 6 + man/iff.Rd |only man/issue_attention_diversity.Rd |only man/mp_nicheness.Rd |only man/prefix.Rd |only vignettes/manifestoRworkflow.Rmd | 14 ++- 25 files changed, 342 insertions(+), 118 deletions(-)
Title: Joint Modelling of the Gene-Expression and Bioassay Data, Taking
Care of the Effect Due to a Fingerprint Feature
Description: Offers modelling the association between gene-expression and bioassay data, taking care of the effect due to a fingerprint feature and helps with several plots to better understand the analysis.
Author: Rudradev Sengupta, Nolen Joy Perualila
Maintainer: Rudradev Sengupta <rudradev.sengupta@uhasselt.be>
Diff between IntegratedJM versions 1.1 dated 2015-09-24 and 1.2 dated 2015-11-12
DESCRIPTION | 16 ++++---- MD5 | 9 ++-- NAMESPACE | 4 +- NEWS | 4 +- R/Functions.R | 112 +++++++++++++++++++++++++++++++++++++++++++++++++++++++-- man/volcano.Rd |only 6 files changed, 128 insertions(+), 17 deletions(-)
Title: Functional Time Series Analysis
Description: Functions for displaying and analyzing functional time series.
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>
Diff between ftsa versions 4.4 dated 2015-08-05 and 4.5 dated 2015-11-12
ftsa-4.4/ftsa/R/ftsmPI.r |only ftsa-4.5/ftsa/ChangeLog | 9 ftsa-4.5/ftsa/DESCRIPTION | 12 - ftsa-4.5/ftsa/MD5 | 76 +++---- ftsa-4.5/ftsa/NAMESPACE | 152 +++++++-------- ftsa-4.5/ftsa/R/T_stationary.R | 280 +++++++++++++--------------- ftsa-4.5/ftsa/R/dynamic_FLR.R |only ftsa-4.5/ftsa/R/farforecast.R | 119 +++++------ ftsa-4.5/ftsa/R/ftsmPI.R |only ftsa-4.5/ftsa/R/pcscorebootstrapdata.R | 122 ++++++------ ftsa-4.5/ftsa/build/vignette.rds |binary ftsa-4.5/ftsa/man/MFDM.Rd | 38 ++- ftsa-4.5/ftsa/man/T_stationary.Rd | 32 +-- ftsa-4.5/ftsa/man/centre.Rd | 58 ++--- ftsa-4.5/ftsa/man/diff.fts.Rd | 4 ftsa-4.5/ftsa/man/dynamic_FLR.Rd |only ftsa-4.5/ftsa/man/dynupdate.Rd | 6 ftsa-4.5/ftsa/man/error.Rd | 2 ftsa-4.5/ftsa/man/extract.Rd | 6 ftsa-4.5/ftsa/man/farforecast.Rd | 24 +- ftsa-4.5/ftsa/man/fbootstrap.Rd | 90 ++++----- ftsa-4.5/ftsa/man/forecast.ftsm.Rd | 12 + ftsa-4.5/ftsa/man/forecastfplsr.Rd | 66 +++--- ftsa-4.5/ftsa/man/fplsr.Rd | 20 +- ftsa-4.5/ftsa/man/ftsa-package.Rd | 6 ftsa-4.5/ftsa/man/ftsm.Rd | 4 ftsa-4.5/ftsa/man/ftsmiterativeforecasts.Rd | 4 ftsa-4.5/ftsa/man/ftsmweightselect.Rd | 2 ftsa-4.5/ftsa/man/isfe.fts.Rd | 2 ftsa-4.5/ftsa/man/mean.fts.Rd | 6 ftsa-4.5/ftsa/man/median.fts.Rd | 6 ftsa-4.5/ftsa/man/pcscorebootstrapdata.Rd | 127 ++++++------ ftsa-4.5/ftsa/man/plot.fmres.Rd | 2 ftsa-4.5/ftsa/man/plot.ftsf.Rd | 2 ftsa-4.5/ftsa/man/plot.ftsm.Rd | 2 ftsa-4.5/ftsa/man/plotfplsr.Rd | 82 ++++---- ftsa-4.5/ftsa/man/pm_10_GR.Rd | 4 ftsa-4.5/ftsa/man/residuals.fm.Rd | 60 +++--- ftsa-4.5/ftsa/man/sd.fts.Rd | 4 ftsa-4.5/ftsa/man/summary.fm.Rd | 2 ftsa-4.5/ftsa/man/var.fts.Rd | 4 41 files changed, 739 insertions(+), 708 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Description: Compare lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard <nicolas.cagnard@gmail.com>
Diff between eVenn versions 2.2.1 dated 2015-10-07 and 2.2.2 dated 2015-11-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/evenn.R | 2 ++ man/eVenn-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Distributed Data Structures in R
Description: Provides distributed data structures and simplifies
distributed computing in R.
Author: Edward Ma, Indrajit Roy, Michael Lawrence
Maintainer: Edward Ma <ema@hpe.com>
Diff between ddR versions 0.1 dated 2015-10-24 and 0.1.1 dated 2015-11-12
ddR-0.1.1/ddR/DESCRIPTION | 9 +++++---- ddR-0.1.1/ddR/MD5 | 21 +++++++++++++-------- ddR-0.1.1/ddR/NEWS.md |only ddR-0.1.1/ddR/README.md | 5 +++++ ddR-0.1.1/ddR/build |only ddR-0.1.1/ddR/inst |only ddR-0.1.1/ddR/man/package.Rd | 16 ++++++++-------- ddR-0.1.1/ddR/vignettes/README.Rmd | 5 +++-- ddR-0.1.1/ddR/vignettes/user_guide.Rmd | 9 +++++---- ddR-0.1/ddR/vignettes/user_guide.html |only ddR-0.1/ddR/vignettes/user_guide.md |only ddR-0.1/ddR/vignettes/user_guide.pdf |only 12 files changed, 39 insertions(+), 26 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre],
Yves Rosseel [aut]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.1 dated 2015-10-07 and 0.1-1 dated 2015-11-12
DESCRIPTION | 10 +-- MD5 | 37 +++++------ NAMESPACE | 4 - NEWS |only R/00class.R | 8 +- R/blav_fit.R | 6 + R/blav_fit_measures.R | 26 ++++--- R/blav_object_methods.R | 56 ++++++++++++---- R/blav_test.R | 15 +++- R/blav_utils.R | 43 ++++++++++++ R/blavaan.R | 138 ++++++++++++++++++++++++++++------------- R/dpriors.R | 4 - R/lav_export_jags.R | 118 ++++++++++++++++++++++++----------- R/set_inits.R | 6 + R/set_priors.R | 159 ++++++++++++++++++++++++++++-------------------- man/bcfa.Rd | 9 ++ man/bgrowth.Rd | 8 +- man/blavaan.Rd | 9 ++ man/bsem.Rd | 9 ++ man/dpriors.Rd | 6 - 20 files changed, 449 insertions(+), 222 deletions(-)
Title: Threshold Estimation
Description: Point and interval estimations of optimum thresholds for continuous diagnostic tests (two- and three- state settings).
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.1 dated 2015-07-12 and 2.2 dated 2015-11-12
DESCRIPTION | 8 MD5 | 14 - R/ThresholdROC-2states.R | 163 ++++++++++--------- R/ThresholdROC-3states.R | 365 +++++++++++++++++++++----------------------- R/diagnostic.R | 52 +++--- man/ThresholdROC-package.Rd | 8 man/diagnostic.Rd | 6 man/lines-thres3.Rd | 2 8 files changed, 316 insertions(+), 302 deletions(-)
Title: Tools for Mapping of Quantitative Traits of Genetically Related
Individuals and Calculating Identity Coefficients from
Pedigrees
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng <riyan.cheng@anu.edu.au>
Maintainer: Riyan Cheng <riyan.cheng@anu.edu.au>
Diff between QTLRel versions 0.2-14 dated 2013-12-11 and 0.2-15 dated 2015-11-12
ChangeLog | 16 ---- DESCRIPTION | 18 ++-- MD5 | 45 ++++++------ NAMESPACE | 12 ++- R/aic.R | 10 ++ R/estVC.R | 34 +++------ R/hapSim.R | 196 ------------------------------------------------------ R/ibsFn.R | 3 R/idcoef.R | 4 - R/imFn.R | 1 R/pedRecode.R |only R/qtl2rel.R | 2 R/rel2qtl.R | 1 R/scan.R | 10 +- data/miscEx.RData |binary man/genoImpute.Rd | 2 man/genoProb.Rd | 6 - man/genoSim.Rd | 4 - man/hapSim.Rd | 4 - man/mAIC.Rd | 2 man/nullSim.Rd | 2 man/plots.Rd | 2 man/rem.Rd | 2 src/rgdat.c | 50 +++++++++---- 24 files changed, 119 insertions(+), 307 deletions(-)
Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Jeroen Ooms [ctb],
Yixuan Qiu [ctb],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.0.4 dated 2015-10-28 and 0.0.5 dated 2015-11-12
DESCRIPTION | 8 +-- MD5 | 20 +++++---- NAMESPACE | 1 NEWS | 5 ++ R/RcppExports.R | 8 +++ R/raster.R | 27 +++++++++++++ inst/include/gdtools_RcppExports.h | 38 ++++++++++++++++++ man/raster_write.Rd |only src/RcppExports.cpp | 76 +++++++++++++++++++++++++++++++++++++ src/raster_to_base64.cpp | 59 ++++++++++++++++++++++++++++ tests |only 11 files changed, 229 insertions(+), 13 deletions(-)
Title: Matrices Backed by Binary PED Files (PLINK)
Description: A matrix-like data structure that allows for efficient,
convenient, and scalable subsetting of binary genotype/phenotype files
generated by PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/), the whole
genome association analysis toolset, without loading the entire file into
memory.
Author: Alexander Grueneberg [aut, cre],
Lian Lian [ctb],
Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between BEDMatrix versions 1.0.0 dated 2015-11-06 and 1.0.1 dated 2015-11-12
DESCRIPTION | 6 MD5 | 11 NEWS.md |only README.md | 20 + configure | 504 +++++++++++++---------------------------- configure.ac | 20 + tools/m4/ax_boost_iostreams.m4 | 8 7 files changed, 215 insertions(+), 354 deletions(-)