Title: R 'Htmlwidget' to Add Pan and Zoom to Almost any R Graphic
Description: This 'htmlwidget' provides pan and zoom interactivity to R
graphics, including 'base', 'lattice', and 'ggplot2'. The interactivity is
provided through the 'svg-pan-zoom.js' library. Various options to the widget
can tailor the pan and zoom experience to nearly any user desire.
Author: Anders Riutta et. al. [aut, cph] (svg-pan-zoom.js BSD-licensed library
in htmlwidgets/lib, https://github.com/ariutta/svg-pan-zoom),
Jorik Tangelder [aut, cph] (hammer.js MIT-licensed touch library in
htmlwidgets/lib, https://github.com/hammerjs/hammer),
Kent Russell [aut, cre] (R interface to svg-pan-zoom.js)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between svgPanZoom versions 0.3.0 dated 2015-09-11 and 0.3.2 dated 2016-03-09
DESCRIPTION | 19 ++--- LICENSE | 2 MD5 | 19 ++--- NAMESPACE | 2 NEWS.md | 11 +++ R/svgPanZoom.R | 29 +++++--- inst/htmlwidgets/lib/svg-pan-zoom/dist/svg-pan-zoom.js |only inst/htmlwidgets/lib/svg-pan-zoom/dist/svg-pan-zoom.min.js | 6 - inst/htmlwidgets/svgPanZoom.js | 45 +++++++------ man/svgPanZoom-shiny.Rd | 6 - man/svgPanZoom.Rd | 29 +++++--- 11 files changed, 100 insertions(+), 68 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Mixed model equation solver allowing the specification of variance covariance structures of random effects and residual structures. ML/REML estimates are obtained using the Average Information and/or Expectation-Maximization algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominant and epistatic relationship structures.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between sommer versions 1.2 dated 2016-02-07 and 1.3 dated 2016-03-09
CHANGELOG | 32 +++ DESCRIPTION | 10 - MD5 | 71 +++---- NAMESPACE | 7 R/AI.R | 62 +++++- R/AI2.R | 397 +++++++++++++++++++++------------------ R/AI3.R | 394 +++++++++++++++++++++------------------ R/D.mat.R | 60 ++---- R/EM.R | 500 ++++++++++++++++++++++++-------------------------- R/EMMA.R | 234 +++++++++++++---------- R/atcg1234.R | 108 ++++++---- R/bag.R |only R/fdr.R | 15 - R/hdm.R | 41 ++-- R/jet.colors.R |only R/mmer.R | 116 +++++++++-- R/mmer2.R | 113 +++++------ R/score.calc.R | 1 man/A.mat.Rd | 4 man/AI.Rd | 46 +++- man/CPdata.Rd | 41 ++-- man/D.mat.Rd | 48 +++- man/E.mat.Rd | 4 man/EM.Rd | 16 + man/EMMA.Rd | 19 + man/HDdata.Rd | 28 ++ man/PolyData.Rd | 45 +++- man/atcg1234.Rd | 8 man/bag.Rd |only man/bathy.colors.Rd |only man/cornHybrid.Rd | 62 +++--- man/fdr.Rd | 11 + man/hdm.Rd | 28 ++ man/jet.colors.Rd |only man/map.plot2.Rd | 9 man/mmer.Rd | 273 +++++++++++++++++++-------- man/mmer2.Rd | 94 ++++++--- man/sommer-package.Rd | 173 +++++++++++------ man/wheatLines.Rd | 57 ++++- 39 files changed, 1895 insertions(+), 1232 deletions(-)
Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow
Archive. The package contains R wrappers to the UK NRFA data temporary-API.
There are functions to retrieve stations falling in a bounding box,
to generate a map and extracting time series and general information.
Author: Claudia Vitolo [aut, cre], Matthew Fry [ctb]
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
Diff between rnrfa versions 0.4.3 dated 2016-02-25 and 0.5.1 dated 2016-03-09
rnrfa-0.4.3/rnrfa/R/CMRmeta.R |only rnrfa-0.4.3/rnrfa/R/CMRmulti.R |only rnrfa-0.4.3/rnrfa/R/GDFmeta.R |only rnrfa-0.4.3/rnrfa/R/GDFmulti.R |only rnrfa-0.4.3/rnrfa/man/CMRmeta.Rd |only rnrfa-0.4.3/rnrfa/man/CMRmulti.Rd |only rnrfa-0.4.3/rnrfa/man/GDFmeta.Rd |only rnrfa-0.4.3/rnrfa/man/GDFmulti.Rd |only rnrfa-0.5.1/rnrfa/DESCRIPTION | 6 +- rnrfa-0.5.1/rnrfa/MD5 | 34 ++++++-------- rnrfa-0.5.1/rnrfa/NAMESPACE | 10 ++-- rnrfa-0.5.1/rnrfa/R/CMR.R | 36 ++++----------- rnrfa-0.5.1/rnrfa/R/FindInfo.R | 41 ++++++++++------- rnrfa-0.5.1/rnrfa/R/GDF.R | 37 ++++----------- rnrfa-0.5.1/rnrfa/R/OSGparse.R | 13 ++--- rnrfa-0.5.1/rnrfa/R/catalogue.R | 81 ++++++++++++++++++++-------------- rnrfa-0.5.1/rnrfa/R/getTS.R |only rnrfa-0.5.1/rnrfa/R/plotRainFlow.R |only rnrfa-0.5.1/rnrfa/man/CMR.Rd | 13 +++-- rnrfa-0.5.1/rnrfa/man/GDF.Rd | 14 +++-- rnrfa-0.5.1/rnrfa/man/OSGparse.Rd | 10 ++-- rnrfa-0.5.1/rnrfa/man/catalogue.Rd | 10 ++-- rnrfa-0.5.1/rnrfa/man/getTS.Rd |only rnrfa-0.5.1/rnrfa/man/plotRainFlow.Rd |only 24 files changed, 153 insertions(+), 152 deletions(-)
Title: Solvers for Large Scale Eigenvalue and SVD Problems
Description: Previously an R wrapper of the 'ARPACK' library
<http://www.caam.rice.edu/software/ARPACK/>, and now a shell of the
R package 'RSpectra', an R interface to the 'Spectra' library
<http://yixuan.cos.name/spectra/> for solving large scale
eigenvalue/vector problems. The current version of 'rARPACK'
simply imports and exports the functions provided by 'RSpectra'.
New users of 'rARPACK' are advised to switch to the 'RSpectra' package.
Author: Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See file
AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between rARPACK versions 0.10-0 dated 2016-01-18 and 0.11-0 dated 2016-03-09
rARPACK-0.10-0/rARPACK/R/10_eigs_real_gen.R |only rARPACK-0.10-0/rARPACK/R/20_eigs_real_sym.R |only rARPACK-0.10-0/rARPACK/R/40_svds_real_gen.R |only rARPACK-0.10-0/rARPACK/R/50_svds_real_sym.R |only rARPACK-0.10-0/rARPACK/R/zzz.R |only rARPACK-0.10-0/rARPACK/inst/include |only rARPACK-0.10-0/rARPACK/src |only rARPACK-0.11-0/rARPACK/DESCRIPTION | 32 ++--- rARPACK-0.11-0/rARPACK/MD5 | 70 +----------- rARPACK-0.11-0/rARPACK/NAMESPACE | 23 ---- rARPACK-0.11-0/rARPACK/R/00_eigs.R | 152 +--------------------------- rARPACK-0.11-0/rARPACK/R/30_svds.R | 40 ------- rARPACK-0.11-0/rARPACK/README.md | 27 +++- rARPACK-0.11-0/rARPACK/inst/NEWS.Rd | 9 + rARPACK-0.11-0/rARPACK/man/eigs.Rd | 44 +------- rARPACK-0.11-0/rARPACK/man/svds.Rd | 18 --- 16 files changed, 72 insertions(+), 343 deletions(-)
Title: Generalized Linear Mixed Model (GLMM) for Binary Randomized
Response Data
Description: Generalized Linear Mixed Model (GLMM) for Binary Randomized Response Data.
Includes Cauchit, Log-Log, Logistic, and Probit link functions for Bernoulli distributed RR data.
Author: Jean-Paul Fox [aut], Konrad Klotzke [aut], Duco Veen [aut]
Maintainer: Konrad Klotzke <omd.bms.utwente.stats@gmail.com>
Diff between GLMMRR versions 0.1.1 dated 2016-03-09 and 0.1.2 dated 2016-03-09
GLMMRR-0.1.1/GLMMRR/R/PlagiarismRR.R |only GLMMRR-0.1.1/GLMMRR/data/PlagiarismRR.rda |only GLMMRR-0.1.1/GLMMRR/man/PlagiarismRR.Rd |only GLMMRR-0.1.2/GLMMRR/DESCRIPTION | 15 GLMMRR-0.1.2/GLMMRR/MD5 | 56 +-- GLMMRR-0.1.2/GLMMRR/NAMESPACE | 48 +- GLMMRR-0.1.2/GLMMRR/R/Plagiarism.R |only GLMMRR-0.1.2/GLMMRR/R/RRglm.R | 218 ++++++------- GLMMRR-0.1.2/GLMMRR/R/RRglmGOF.R | 416 ++++++++++++------------- GLMMRR-0.1.2/GLMMRR/R/RRglmer.R | 268 ++++++++-------- GLMMRR-0.1.2/GLMMRR/R/RRlink_cauchit.R | 56 +-- GLMMRR-0.1.2/GLMMRR/R/RRlink_cloglog.R | 56 +-- GLMMRR-0.1.2/GLMMRR/R/RRlink_logit.R | 56 +-- GLMMRR-0.1.2/GLMMRR/R/RRlink_probit.R | 56 +-- GLMMRR-0.1.2/GLMMRR/R/getRRparameters.R | 270 ++++++++-------- GLMMRR-0.1.2/GLMMRR/R/hello.R | 8 GLMMRR-0.1.2/GLMMRR/R/print.R | 124 +++---- GLMMRR-0.1.2/GLMMRR/R/summary.R | 422 +++++++++++++------------- GLMMRR-0.1.2/GLMMRR/data/Plagiarism.rda |only GLMMRR-0.1.2/GLMMRR/man/Plagiarism.Rd |only GLMMRR-0.1.2/GLMMRR/man/RRglm.Rd | 104 +++--- GLMMRR-0.1.2/GLMMRR/man/RRglmGOF.Rd | 88 ++--- GLMMRR-0.1.2/GLMMRR/man/RRglmer.Rd | 128 +++---- GLMMRR-0.1.2/GLMMRR/man/RRlink.cauchit.Rd | 42 +- GLMMRR-0.1.2/GLMMRR/man/RRlink.cloglog.Rd | 42 +- GLMMRR-0.1.2/GLMMRR/man/RRlink.logit.Rd | 42 +- GLMMRR-0.1.2/GLMMRR/man/RRlink.probit.Rd | 42 +- GLMMRR-0.1.2/GLMMRR/man/getRRparameters.Rd | 48 +- GLMMRR-0.1.2/GLMMRR/man/hello.Rd | 24 - GLMMRR-0.1.2/GLMMRR/man/print.RRglmGOF.Rd | 38 +- GLMMRR-0.1.2/GLMMRR/man/summary.RRglm.Rd | 48 +- GLMMRR-0.1.2/GLMMRR/man/summary.RRglmerMod.Rd | 48 +- 32 files changed, 1385 insertions(+), 1378 deletions(-)
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Description: Automated General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean.
Author: Genaro Sucarrat [aut, cre], Felix Pretis [aut], James Reade [aut]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between gets versions 0.5 dated 2016-02-28 and 0.6 dated 2016-03-09
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ NEWS | 18 +++++++++++++++--- R/isat.R | 4 +++- man/coef.arx.Rd | 2 +- man/coef.gets.Rd | 24 +++++------------------- man/gets-package.Rd | 4 ++-- man/paths.Rd |only 8 files changed, 38 insertions(+), 37 deletions(-)
Title: Fuzzy Forests
Description: Fuzzy forests, a new algorithm based on random forests,
is designed to reduce the bias seen in random forest feature selection
caused by the presence of correlated features. Fuzzy forests uses
recursive feature elimination random forests to select
features from separate blocks of correlated features where the
correlation within each block of features is high
and the correlation between blocks of features is low.
One final random forest is fit using the surviving features.
This package fits random forests using the 'randomForest' package and
allows for easy use of 'WGCNA' to split features into distinct blocks.
Author: Daniel Conn [aut, cre],
Tuck Ngun [aut],
Christina M. Ramirez [aut]
Maintainer: Daniel Conn <djconn17@gmail.com>
Diff between fuzzyforest versions 1.0.0 dated 2016-02-18 and 1.0.1 dated 2016-03-09
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/select_RF.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Time-Dependent ROC Curve Estimators and Expected Utility
Functions
Description: Contains functions in order to estimate diagnostic and prognostic capacities of continuous markers. More precisely, one function concerns the estimation of time-dependent ROC (ROCt) curve, as proposed by Heagerty et al. (2000) <DOI: 10.1111/j.0006-341X.2000.00337.x>. One function concerns the adaptation of the ROCt theory for studying the capacity of a marker to predict the excess of mortality of a specific population compared to the general population. This last part is based on additive relative survival models and the work of Pohar-Perme et al. (2012) <DOI: 10.1111/j.1541-0420.2011.01640.x>. We also propose two functions for cut-off estimation in medical decision making by maximizing time-dependent expected utility function. Finally, we propose confounder-adjusted estimators of ROC and ROCt curves by using the Inverse Probability Weighting (IPW) approach. For the confounder-adjusted ROC curve (without censoring), we also proposed the implementation of the estimator based on placement values proposed by Pepe and Cai (2004) <DOI: 10.1111/j.0006-341X.2004.00200.x>.
Author: Y. Foucher, E. Dantan, P. Tessier, F. Le Borgne, and M. Lorent
Maintainer: Y. Foucher <Yohann.Foucher@univ-nantes.fr>
Diff between ROCt versions 0.8 dated 2013-12-20 and 0.9.4 dated 2016-03-09
ROCt-0.8/ROCt/man/allcause.ROCt.Rd |only ROCt-0.9.4/ROCt/DESCRIPTION | 18 ROCt-0.9.4/ROCt/MD5 | 33 - ROCt-0.9.4/ROCt/NAMESPACE | 7 ROCt-0.9.4/ROCt/R/prog.R | 666 +++++++++++++++++++++++++++++++- ROCt-0.9.4/ROCt/data/dataDIVAT.rda |binary ROCt-0.9.4/ROCt/data/dataKTFS.rda |only ROCt-0.9.4/ROCt/data/datalist | 1 ROCt-0.9.4/ROCt/data/fr.ratetable.rda |binary ROCt-0.9.4/ROCt/data/rein.ratetable.rda |binary ROCt-0.9.4/ROCt/man/AUC.Rd |only ROCt-0.9.4/ROCt/man/EUt1.Rd |only ROCt-0.9.4/ROCt/man/EUt2.Rd |only ROCt-0.9.4/ROCt/man/ROCt-package.Rd | 37 + ROCt-0.9.4/ROCt/man/adjusted.ROC.Rd |only ROCt-0.9.4/ROCt/man/adjusted.ROCt.Rd |only ROCt-0.9.4/ROCt/man/crude.ROCt.Rd |only ROCt-0.9.4/ROCt/man/dataDIVAT.Rd | 4 ROCt-0.9.4/ROCt/man/dataKTFS.Rd |only ROCt-0.9.4/ROCt/man/fr.ratetable.Rd | 8 ROCt-0.9.4/ROCt/man/net.ROCt.Rd | 57 +- ROCt-0.9.4/ROCt/man/rein.ratetable.Rd | 6 22 files changed, 738 insertions(+), 99 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic agent-based, and stochastic network models. Network models use
robust statistical methods of exponential-family random graph models (ERGMs)
from the Statnet suite of software packages in R. Standard templates for epidemic
modeling include SI, SIR, and SIS disease types. EpiModel features
an easy API for extending these templates to address novel scientific research
aims.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Li Wang [ctb],
Skye Bender-deMoll [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>
Diff between EpiModel versions 1.2.4 dated 2016-02-01 and 1.2.5 dated 2016-03-09
DESCRIPTION | 8 - MD5 | 59 +++++----- NEWS | 15 ++ R/EpiModel-package.r | 4 R/control.R | 5 R/dendo.R | 195 ++++++++++++++++++++++------------ R/netdx.R | 3 R/netest.R | 22 --- R/netsim.R | 141 ++++++++++++++++-------- R/param.R | 3 R/test.R | 140 ++++++------------------ inst/doc/Intro.Rmd | 2 inst/doc/Intro.html | 21 +-- man/EpiModel-package.Rd | 4 man/as.network.transmat.Rd | 2 man/as.phylo.transmat.Rd | 32 +++-- man/control.net.Rd | 25 ++-- man/netest.Rd | 7 - man/netsim.Rd | 9 - man/param.net.Rd | 3 man/plot.transmat.Rd | 2 tests/testthat/test-dcm.R | 11 + tests/testthat/test-icm-long.R | 5 tests/testthat/test-icm.R | 23 ++++ tests/testthat/test-netdx.R | 46 +++++++- tests/testthat/test-netest.R | 55 +++++++++ tests/testthat/test-netsim-parallel.R |only tests/testthat/test-netsim.R | 51 ++++++++ tests/testthat/test-print.R | 30 ++--- tests/testthat/test-transmat-dendo.R | 26 ++++ vignettes/Intro.Rmd | 2 31 files changed, 598 insertions(+), 353 deletions(-)
Title: Discover Probable Duplicates in Plant Genetic Resources
Collections
Description: Provides functions to aid the identification of probable/possible
duplicates in Plant Genetic Resources (PGR) collections using
'passport databases' comprising of information records of each constituent
sample. These include methods for cleaning the data, creation of a
searchable Key Word in Context (KWIC) index of keywords associated with
sample records and the identification of nearly identical records with
similar information by fuzzy, phonetic and semantic matching of keywords.
Author: J. Aravind [aut, cre],
J. Radhamani [aut],
Kalyani Srinivasan [aut],
B. Ananda Subhash [aut],
R. K. Tyagi [aut]
Maintainer: J. Aravind <j.aravind@icar.gov.in>
Diff between PGRdup versions 0.2.2 dated 2016-03-05 and 0.2.2.1 dated 2016-03-09
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/fdouble_metaphone.c | 14 +++++--------- 3 files changed, 10 insertions(+), 14 deletions(-)
Title: Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal
Testing
Description: Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal
Testing.
Author: Dirk de Weerd, Lennart Johansson
Maintainer: Lennart Johansson <l.johansson@umcg.nl>
Diff between NIPTeR versions 1.0.1 dated 2016-01-02 and 1.0.2 dated 2016-03-09
DESCRIPTION | 14 +++---- MD5 | 22 +++++------ NAMESPACE | 1 R/bin_sample.R | 1 R/diagnose_control_group.R | 2 - R/prepare_ncv_template.R | 14 +++---- R/regression.R | 4 +- R/z_score.R | 2 - build/vignette.rds |binary inst/doc/NIPTeR.Rmd | 2 - inst/doc/NIPTeR.html | 84 +++++++++++++++++++++++++++++++++++---------- vignettes/NIPTeR.Rmd | 2 - 12 files changed, 98 insertions(+), 50 deletions(-)
Title: Simple Metrics to Summarize Growth Curves
Description: This is a simple package that fits the logistic equation to
microbial growth curve data (e.g., repeated absorbance measurements
taken from a plate reader over time). From this fit, a variety of
metrics are provided, including the maximum growth rate,
the doubling time, the carrying capacity, the area under the logistic
curve, and the time to the inflection point.
Author: Kathleen sprouffske [aut, cre]
Maintainer: Kathleen sprouffske <sprouffske@gmail.com>
Diff between growthcurver versions 0.1.0 dated 2015-11-03 and 0.2.0 dated 2016-03-09
DESCRIPTION | 12 - MD5 | 26 +-- NAMESPACE | 1 R/fit-logistic.R | 4 R/helpers.R | 42 +++++ R/summarize-growth-by-plate.R |only R/summarize-growth.R | 82 +++++++++-- README.md | 6 inst/doc/Growthcurver-vignette.R | 136 ++++++++++++------ inst/doc/Growthcurver-vignette.Rmd | 190 +++++++++++++++++--------- inst/doc/Growthcurver-vignette.html | 247 +++++++++++++++++++++++++--------- man/SummarizeGrowth.Rd | 18 ++ man/SummarizeGrowthByPlate.Rd |only tests/testthat/test_SummarizeGrowth.R | 2 vignettes/Growthcurver-vignette.Rmd | 190 +++++++++++++++++--------- 15 files changed, 686 insertions(+), 270 deletions(-)
Title: Emoji Fonts for using in R
Description: An implementation of using emoji font in both base and 'ggplot2' graphics.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between emojifont versions 0.3.1 dated 2016-02-26 and 0.3.2 dated 2016-03-09
DESCRIPTION | 6 - MD5 | 14 ++- README.md | 130 +++++-------------------------------- build/vignette.rds |binary inst/doc/emojifont.Rmd | 40 ++++++++++- inst/doc/emojifont.html | 72 +++++++++++++++----- vignettes/emojifont.Rmd | 40 ++++++++++- vignettes/figures/apple_emoji2.png |only vignettes/figures/fontawesome.png |only 9 files changed, 159 insertions(+), 143 deletions(-)
Title: Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
Description: We implemented a Bayesian-statistics approach for
subtraction of incoherent scattering from neutron total-scattering data.
In this approach, the estimated background signal associated with
incoherent scattering maximizes the posterior probability, which combines
the likelihood of this signal in reciprocal and real spaces with the prior
that favors smooth lines.
Author: Anton Gagin and Igor Levin with contributions from Charles R. Hogg III
Maintainer: Anton Gagin <av.gagin@gmail.com>
Diff between BBEST versions 0.1-5 dated 2015-09-15 and 0.1-6 dated 2016-03-09
ChangeLog | 9 DESCRIPTION | 8 MD5 | 16 - README.md | 6 inst/gui/help/help.html | 540 ++++++++++++++++++++++++------------------------ inst/gui/server.R | 31 ++ inst/gui/ui.R | 3 man/do.fit.Rd | 2 man/set.control.Rd | 2 9 files changed, 326 insertions(+), 291 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.5.4 dated 2016-01-16 and 0.5.6 dated 2016-03-09
DESCRIPTION | 8 +- MD5 | 56 ++++++++--------- R/linarpr.R | 8 -- R/linarpt.R | 5 - R/linarr.R | 31 ++++----- R/lingini.R | 18 ++--- R/lingini2.R | 18 ++--- R/lingpg.R | 55 ++++++++-------- R/linpoormed.R | 9 +- R/linqsr.R | 132 ++++++++++++++++++++-------------------- R/linrmir.R | 8 -- R/linrmpg.R | 5 - R/vardchangannual.R | 16 ++-- R/vardchanges.R | 157 ++++++++++++++++++++++++++---------------------- R/vardchangespoor.R | 102 +++++++++++++++++-------------- R/vardcros.R | 49 ++++++-------- R/vardcrospoor.R | 19 +---- R/vardomh.R | 7 +- R/variance_est.R | 26 +++---- R/variance_othstr.R | 86 ++++++++++---------------- R/varpoord.R | 8 +- inst/CITATION | 4 - inst/NEWS | 9 ++ man/vardchangannual.Rd | 5 - man/vardchanges.Rd | 8 -- man/vardchangespoor.Rd | 6 - man/vardcros.Rd | 9 -- man/vardcrospoor.Rd | 5 - man/vardpoor-package.Rd | 4 - 29 files changed, 420 insertions(+), 453 deletions(-)
Title: Global, Parameterwise and Joint Shrinkage Factor Estimation
Description: The predictive value of a statistical model can often be improved
by applying shrinkage methods. This can be achieved, e.g., by regularized
regression or empirical Bayes approaches. Various types of shrinkage factors can
also be estimated after a maximum likelihood. While global shrinkage modifies
all regression coefficients by the same factor, parameterwise shrinkage factors
differ between regression coefficients. With variables which are either highly
correlated or associated with regard to contents, such as several columns of a
design matrix describing a nonlinear effect, parameterwise shrinkage factors are
not interpretable and a compromise between global and parameterwise shrinkage,
termed 'joint shrinkage', is a useful extension. A computational shortcut to
resampling-based shrinkage factor estimation based on DFBETA residuals can be
applied. Global, parameterwise and joint shrinkage for models fitted by lm(),
glm(), coxph(), or mfp() is available.
Author: Daniela Dunkler [aut, cre],
Georg Heinze [aut]
Maintainer: Daniela Dunkler <daniela.dunkler@meduniwien.ac.at>
Diff between shrink versions 1.2.0 dated 2014-10-02 and 1.2.1 dated 2016-03-09
shrink-1.2.0/shrink/Changelog |only shrink-1.2.0/shrink/R/additionalfunctions.r |only shrink-1.2.0/shrink/R/coef.shrink.r |only shrink-1.2.0/shrink/R/predict.shrink.r |only shrink-1.2.0/shrink/R/print.shrink.r |only shrink-1.2.0/shrink/R/shrink.coxph.r |only shrink-1.2.0/shrink/R/shrink.glm.r |only shrink-1.2.0/shrink/R/shrink.lm.r |only shrink-1.2.0/shrink/R/shrink.r |only shrink-1.2.0/shrink/R/summary.shrink.r |only shrink-1.2.0/shrink/R/vcov.shrink.r |only shrink-1.2.0/shrink/data/GBSG.txt.gz |only shrink-1.2.0/shrink/data/deepvein.txt.gz |only shrink-1.2.1/shrink/DESCRIPTION | 49 ++- shrink-1.2.1/shrink/MD5 | 62 ++-- shrink-1.2.1/shrink/NAMESPACE | 41 ++- shrink-1.2.1/shrink/R/GBSG.R |only shrink-1.2.1/shrink/R/coef.shrink.R |only shrink-1.2.1/shrink/R/deepvein.R |only shrink-1.2.1/shrink/R/predict.shrink.R |only shrink-1.2.1/shrink/R/print.shrink.R |only shrink-1.2.1/shrink/R/shrink.R |only shrink-1.2.1/shrink/R/shrink.coxph.R |only shrink-1.2.1/shrink/R/shrink.glm.R |only shrink-1.2.1/shrink/R/shrink.lm.R |only shrink-1.2.1/shrink/R/summary.shrink.R |only shrink-1.2.1/shrink/R/utility.R |only shrink-1.2.1/shrink/R/vcov.shrink.R |only shrink-1.2.1/shrink/R/zzz.R |only shrink-1.2.1/shrink/build |only shrink-1.2.1/shrink/data/GBSG.rda |only shrink-1.2.1/shrink/data/deepvein.rda |only shrink-1.2.1/shrink/inst/CITATION | 40 +-- shrink-1.2.1/shrink/inst/NEWS.Rd |only shrink-1.2.1/shrink/inst/doc |only shrink-1.2.1/shrink/man/GBSG.Rd | 62 ++-- shrink-1.2.1/shrink/man/coef.shrink.Rd | 49 +-- shrink-1.2.1/shrink/man/deepvein.Rd | 120 +++------ shrink-1.2.1/shrink/man/isrcs.Rd |only shrink-1.2.1/shrink/man/predict.shrink.Rd | 124 ++++++--- shrink-1.2.1/shrink/man/print.shrink.Rd | 46 +-- shrink-1.2.1/shrink/man/shrink-package.Rd | 116 ++++---- shrink-1.2.1/shrink/man/shrink.Rd | 361 ++++++++++++++-------------- shrink-1.2.1/shrink/man/shrink.coxph.Rd |only shrink-1.2.1/shrink/man/shrink.glm.Rd |only shrink-1.2.1/shrink/man/shrink.lm.Rd |only shrink-1.2.1/shrink/man/summary.shrink.Rd | 52 +--- shrink-1.2.1/shrink/man/vcov.shrink.Rd | 50 +-- shrink-1.2.1/shrink/vignettes |only 49 files changed, 595 insertions(+), 577 deletions(-)
Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. Both Markov
transition rates and the hidden Markov output process can be modelled
in terms of covariates, which may be constant or piecewise-constant
in time.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between msm versions 1.6 dated 2015-11-18 and 1.6.1 dated 2016-03-09
ChangeLog | 21 ++++++++++++++ DESCRIPTION | 8 ++--- MD5 | 36 ++++++++++++------------ R/draic.R | 9 ++++-- R/hmm.R | 5 ++- R/msm.R | 50 ++++++++++++++++++++++++++------- build/vignette.rds |binary inst/NEWS | 15 ++++++++++ inst/doc/msm-manual.pdf |binary man/draic.msm.Rd | 8 ++++- man/msm.Rd | 30 ++++++++++---------- src/lik.c | 7 ++-- src/msm.h | 1 tests/testthat/helper.r | 9 +----- tests/testthat/test_datasumm.r | 2 - tests/testthat/test_deriv.r | 51 +++++++++++++++++----------------- tests/testthat/test_models.r | 7 +++- tests/testthat/test_models_hmmmulti.r | 11 ++++--- tests/testthat/test_models_misc.r | 5 +++ 19 files changed, 179 insertions(+), 96 deletions(-)
Title: Functional Data Analysis and Partial Differential Equations;
Statistical Analysis of Functional and Spatial Data, Based on
Regression with Partial Differential Regularizations
Description: An implementation of regression models with partial differential regularizations, making use of the Finite Element Method. The models efficiently handle data distributed over irregularly shaped domains and can comply with various conditions at the boundaries of the domain. A priori information about the spatial structure of the phenomenon under study can be incorporated in the model via the differential regularization.
Author: Eardi Lila [aut, cre],
Laura M. Sangalli [aut],
Jim Ramsay [aut],
Luca Formaggia [aut]
Maintainer: Eardi Lila <el425@cam.ac.uk>
Diff between fdaPDE versions 0.1-1 dated 2016-01-15 and 0.1-2 dated 2016-03-09
DESCRIPTION | 18 ++--- MD5 | 88 +++++++++++++------------ R/fdaPDE.checkParameters.R |only R/fdaPDE.locator.R | 23 ++++-- R/fdaPDE.objects.R | 41 ++++++------ R/fdaPDE.smoothing.R | 133 ++++++++++++++++++++++++++++++--------- R/fdaPDE.smoothing_CPP.R | 6 - R/fdaPDE.smoothing_R.R | 14 +++- R/mesh.2D.R | 29 +++----- README.md |only man/FEM.Rd | 8 +- man/MeuseBorder.Rd | 2 man/MeuseData.Rd | 8 +- man/R_elementProperties.Rd | 8 +- man/R_eval.FEM.Rd | 4 - man/R_eval.FEM.basis.Rd | 6 - man/R_mass.Rd | 4 - man/R_smooth.FEM.basis.Rd | 4 - man/R_stiff.Rd | 4 - man/create.FEM.basis.Rd | 28 +++----- man/create.MESH.2D.Rd | 32 ++++----- man/eval.FEM.Rd | 4 - man/image.FEM.Rd | 4 - man/mesh.2D.rectangular.Rd | 2 man/mesh.2D.simple.Rd | 2 man/plot.FEM.Rd | 4 - man/plot.MESH2D.Rd | 2 man/refine.MESH.2D.Rd | 18 ++--- man/smooth.FEM.PDE.basis.Rd | 29 ++++---- man/smooth.FEM.PDE.sv.basis.Rd | 51 +++++++++----- man/smooth.FEM.basis.Rd | 27 ++++--- src/FEMeval.cpp | 3 src/evaluator.h | 2 src/evaluator_imp.h | 30 +++++--- src/fdaPDE.cpp | 50 +++++++------- src/finite_element_imp.h | 7 +- src/mesh.h | 2 src/mesh_imp.h | 41 ++++++------ src/mesh_objects.h | 1 src/mesh_objects_imp.h | 10 +- src/mixedFERegression_imp.h | 31 +++++---- src/triangle.c | 1 tests/testsmoothingPDE.R | 2 tests/testsmoothingPDESV.R | 14 ++-- tests/testsmoothingbaseCPPcode.R | 2 tests/testsmoothingbaseRcode.R | 2 46 files changed, 470 insertions(+), 331 deletions(-)
Title: Simulation of Time-to-Event Family Data and Penetrance
Estimation
Description: Generates time-to-event family data associated with mutated genes arising from various family study designs such as population-based, clinic- based, or multi-stage designs and provides functions to fit family data accounting for the study design and estimate age-dependent penetrance functions. It also provides carrier probabilities for those with missing genotypes and penetrance estimations are based on an Expectation-Maximization algorithm when genotypes are missing.
Author: Yun-Hee Choi, Karen Kopciuk, Wenqing He, Laurent Briollais
Maintainer: Yun-Hee Choi <yun-hee.choi@schulich.uwo.ca>
Diff between FamEvent versions 1.0 dated 2016-02-09 and 1.1 dated 2016-03-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/inv.surv.R | 2 +- R/penmodelEM.R | 15 ++++++++++----- R/plot.simfam.R | 14 ++++++++------ man/plot.simfam.Rd | 19 +++++++++---------- man/simfam.Rd | 2 +- 7 files changed, 39 insertions(+), 33 deletions(-)
Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files, calculate DVH
metrics as well as generalized equivalent uniform dose (gEUD),
biologically effective dose (BED), equivalent dose in 2 Gy
fractions (EQD2), normal tissue complication probability
(NTCP), and tumor control probability (TCP). Show DVH
diagrams, check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>
Diff between DVHmetrics versions 0.3.4 dated 2015-11-27 and 0.3.5 dated 2016-03-09
DVHmetrics-0.3.4/DVHmetrics/R/loessSelSpan.R |only DVHmetrics-0.3.5/DVHmetrics/DESCRIPTION | 10 - DVHmetrics-0.3.5/DVHmetrics/MD5 | 68 +++--- DVHmetrics-0.3.5/DVHmetrics/NAMESPACE | 95 +++++---- DVHmetrics-0.3.5/DVHmetrics/R/convertDVH.R | 178 ++++++------------ DVHmetrics-0.3.5/DVHmetrics/R/convertDVHsmooth.R |only DVHmetrics-0.3.5/DVHmetrics/R/getDMEAN.R | 51 +++-- DVHmetrics-0.3.5/DVHmetrics/R/getHI.R |only DVHmetrics-0.3.5/DVHmetrics/R/getMeanDVH.R | 20 -- DVHmetrics-0.3.5/DVHmetrics/R/getMetric.R | 36 ++- DVHmetrics-0.3.5/DVHmetrics/R/getNTCP.R | 5 DVHmetrics-0.3.5/DVHmetrics/R/parseCadplan.R | 4 DVHmetrics-0.3.5/DVHmetrics/R/parseConstraint.R | 7 DVHmetrics-0.3.5/DVHmetrics/R/parseEclipse.R | 4 DVHmetrics-0.3.5/DVHmetrics/R/parseHiArt.R | 15 - DVHmetrics-0.3.5/DVHmetrics/R/parseMasterplan.R | 4 DVHmetrics-0.3.5/DVHmetrics/R/parseMetric.R | 21 +- DVHmetrics-0.3.5/DVHmetrics/R/parseMonaco.R | 31 ++- DVHmetrics-0.3.5/DVHmetrics/R/parsePinnacleDVH.R | 33 +-- DVHmetrics-0.3.5/DVHmetrics/R/parseRayStation.R | 4 DVHmetrics-0.3.5/DVHmetrics/R/showDVH.R | 2 DVHmetrics-0.3.5/DVHmetrics/R/smoothDVH.R | 2 DVHmetrics-0.3.5/DVHmetrics/inst/ChangeLog | 27 ++ DVHmetrics-0.3.5/DVHmetrics/inst/DVHshiny/helper.R | 5 DVHmetrics-0.3.5/DVHmetrics/inst/DVHshiny/server.R | 12 - DVHmetrics-0.3.5/DVHmetrics/inst/DVHshiny/ui.R | 25 +- DVHmetrics-0.3.5/DVHmetrics/inst/doc/DVHmetrics.Rnw | 3 DVHmetrics-0.3.5/DVHmetrics/inst/doc/DVHmetrics.pdf |binary DVHmetrics-0.3.5/DVHmetrics/inst/doc/DVHshiny.pdf |binary DVHmetrics-0.3.5/DVHmetrics/man/DVHmetrics-package.Rd | 4 DVHmetrics-0.3.5/DVHmetrics/man/convertDVH.Rd | 17 - DVHmetrics-0.3.5/DVHmetrics/man/convertDVHsmooth.Rd |only DVHmetrics-0.3.5/DVHmetrics/man/getDMEAN.Rd | 3 DVHmetrics-0.3.5/DVHmetrics/man/getMeanDVH.Rd | 13 - DVHmetrics-0.3.5/DVHmetrics/man/getMetric.Rd | 1 DVHmetrics-0.3.5/DVHmetrics/man/readDVH.Rd | 2 DVHmetrics-0.3.5/DVHmetrics/vignettes/DVHmetrics.Rnw | 3 37 files changed, 374 insertions(+), 331 deletions(-)
Title: Automated C Code Generation for Use with the 'deSolve' and
'bvpSolve' Packages
Description: Generates all necessary C functions allowing the user to work with the compiled-code interface of ode() and bvptwp(). The implementation supports "forcings" and "events". Also provides functions to symbolically compute Jacobians, sensitivity equations and adjoint sensitivities being the basis for sensitivity analysis.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@physik.uni-freiburg.de>
Diff between cOde versions 0.2 dated 2015-06-10 and 0.2.1 dated 2016-03-09
cOde-0.2.1/cOde/DESCRIPTION | 8 ++++---- cOde-0.2.1/cOde/MD5 | 14 ++++++-------- cOde-0.2.1/cOde/NAMESPACE | 3 +++ cOde-0.2.1/cOde/R/cOde.R | 22 +++++++++++++++------- cOde-0.2.1/cOde/R/derivedEquations.R | 2 +- cOde-0.2.1/cOde/R/symbolics.R | 7 ++++--- cOde-0.2.1/cOde/man/funC.Rd | 5 ++++- cOde-0.2/cOde/data |only 8 files changed, 37 insertions(+), 24 deletions(-)
Title: Recovering a Basic Space from Issue Scales
Description: Conducts Aldrich-McKelvey and Blackbox Scaling to Recover
Latent Dimensions of Judgment.
Author: Keith Poole <ktpoole@uga.edu>, Howard Rosenthal
<hr31@nyu.edu>, Jeffrey Lewis <jblewis@ucla.edu>,
James Lo <jameslo@princeton.edu> and Royce Carroll
<rcarroll@rice.edu>
Maintainer: James Lo <jameslo@princeton.edu>
Diff between basicspace versions 0.15 dated 2014-11-19 and 0.17 dated 2016-03-09
ChangeLog | 17 +++++------------ DESCRIPTION | 10 +++++----- MD5 | 20 +++++++++++--------- NAMESPACE | 11 +++++++++++ build |only inst/CITATION |only man/Issues1980.Rd | 2 +- man/LC1980.Rd | 2 +- man/aldmck.Rd | 6 +++++- man/blackbox.Rd | 4 ++++ man/blackbox_transpose.Rd | 4 ++++ man/boot_aldmck.Rd | 6 +++++- 12 files changed, 52 insertions(+), 30 deletions(-)
Title: Hierarchical Models for Parametric and Semi-Parametric Analyses
of Semi-Competing Risks Data
Description: Parametric and semi-parametric analyses of semi-competing risks/univariate survival data.
Author: Kyu Ha Lee and Sebastien Haneuse
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>
Diff between SemiCompRisks versions 2.3 dated 2015-12-04 and 2.4 dated 2016-03-09
DESCRIPTION | 10 MD5 | 18 - R/BayesID.R | 80 +++---- R/BayesSurv.R | 28 +- R/initiate.startValues.R | 442 +++++++++++++++++++++++++++++++++++-------- R/methods.R | 169 ++++++++++++---- man/BayesID.Rd | 10 man/BayesSurv.Rd | 10 man/SemiCompRisks-package.Rd | 8 man/initiate.startValues.Rd | 39 +++ 10 files changed, 614 insertions(+), 200 deletions(-)
Title: Read ODS Files
Description: Read ODS (OpenDocument Spreadsheet) and puts them into data frames.
Author: Gerrit-Jan Schutten, Chung-hong Chan
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between readODS versions 1.4 dated 2014-07-07 and 1.6.2 dated 2016-03-09
readODS-1.4/readODS/man/getNrOfSheetsInODS.Rd |only readODS-1.4/readODS/man/getODSRoot.Rd |only readODS-1.4/readODS/man/lettersToNumber.Rd |only readODS-1.4/readODS/man/numberToLetters.Rd |only readODS-1.4/readODS/man/odsPreParser.Rd |only readODS-1.4/readODS/tests/runAllTests.R |only readODS-1.4/readODS/tests/testdata/content_googledocs.xml |only readODS-1.4/readODS/tests/testdata/content_layout_test.xml |only readODS-1.4/readODS/tests/testdata/content_lotsofnothing_test.xml |only readODS-1.4/readODS/tests/testdata/content_mergerandgreaterthanlibreoffice.xml |only readODS-1.4/readODS/tests/testdata/content_multisheet.xml |only readODS-1.4/readODS/tests/testdata/content_sum.xml |only readODS-1.4/readODS/tests/testdata/content_table.xml |only readODS-1.4/readODS/tests/testdata/content_test.xml |only readODS-1.4/readODS/tests/testthat/test_readODS.R |only readODS-1.6.2/readODS/DESCRIPTION | 24 readODS-1.6.2/readODS/MD5 | 35 readODS-1.6.2/readODS/NAMESPACE | 9 readODS-1.6.2/readODS/R/readODS.R | 679 +++------- readODS-1.6.2/readODS/README.md | 91 - readODS-1.6.2/readODS/man/get_num_sheet_in_ods.Rd |only readODS-1.6.2/readODS/man/ods_sheets.Rd |only readODS-1.6.2/readODS/man/read.ods.Rd | 18 readODS-1.6.2/readODS/man/read_ods.Rd |only readODS-1.6.2/readODS/tests/testdata/1996-2000.ods |only readODS-1.6.2/readODS/tests/testdata/datasets.ods |only readODS-1.6.2/readODS/tests/testdata/merged.ods |only readODS-1.6.2/readODS/tests/testdata/smartSheetTest.ods |only readODS-1.6.2/readODS/tests/testthat.R |only readODS-1.6.2/readODS/tests/testthat/test_legacy.R |only readODS-1.6.2/readODS/tests/testthat/test_read_ods.R |only 31 files changed, 345 insertions(+), 511 deletions(-)
Title: Unified Handling of Graphics Devices
Description: Functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.devices versions 2.13.2 dated 2015-12-16 and 2.14.0 dated 2016-03-09
DESCRIPTION | 8 - MD5 | 30 ++-- NAMESPACE | 1 NEWS | 10 + R/capturePlot.R |only R/devOptions.R | 6 R/deviceUtils.R | 24 +++ R/utils.R |only build/vignette.rds |binary inst/doc/R.devices-overview.pdf |binary man/R.devices-package.Rd | 4 man/capturePlot.Rd |only tests/capabilitiesX11.R | 2 tests/capturePlot.R |only tests/devEqualTypes.R | 82 ++++++------- tests/devEval.R | 4 tests/devNew.R | 242 ++++++++++++++++++++-------------------- tests/toNNN.R | 57 ++++----- 18 files changed, 250 insertions(+), 220 deletions(-)
Title: Bindings to AppArmor and Security Related Linux Tools
Description: Bindings to various methods in the kernel for enforcing security
restrictions. AppArmor can apply mandatory access control (MAC) policies on
a given task (process) via security profiles with detailed ACL definitions.
In addition the package has kernel bindings for setting the process hardware
resource limits (rlimit), uid, gid, affinity and priority. The high level R
function 'eval.secure' builds on these methods to do dynamic sandboxing:
it evaluates a single R expression within a temporary fork which acts as a
sandbox by enforcing fine grained restrictions without affecting the main R
process.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between RAppArmor versions 1.0.1 dated 2013-12-18 and 2.0 dated 2016-03-09
RAppArmor-1.0.1/RAppArmor/R/aa_change_hat.R |only RAppArmor-1.0.1/RAppArmor/R/aa_change_profile.R |only RAppArmor-1.0.1/RAppArmor/R/aa_find_mountpoint.R |only RAppArmor-1.0.1/RAppArmor/R/aa_getcon.R |only RAppArmor-1.0.1/RAppArmor/R/aa_is_enabled.R |only RAppArmor-1.0.1/RAppArmor/R/errno.R |only RAppArmor-1.0.1/RAppArmor/R/kill.R |only RAppArmor-1.0.1/RAppArmor/R/ncores.R |only RAppArmor-1.0.1/RAppArmor/R/setaffinity.R |only RAppArmor-1.0.1/RAppArmor/R/setgid.R |only RAppArmor-1.0.1/RAppArmor/R/setpgid.R |only RAppArmor-1.0.1/RAppArmor/R/setpriority.R |only RAppArmor-1.0.1/RAppArmor/R/setuid.R |only RAppArmor-1.0.1/RAppArmor/inst/doc/v55i07.Rnw |only RAppArmor-1.0.1/RAppArmor/inst/tests |only RAppArmor-1.0.1/RAppArmor/man/kill.Rd |only RAppArmor-1.0.1/RAppArmor/man/ncores.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_as.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_core.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_cpu.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_data.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_fsize.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_memlock.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_msgqueue.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_nice.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_nofile.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_nproc.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_rtprio.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_rttime.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_sigpending.Rd |only RAppArmor-1.0.1/RAppArmor/man/rlimit_stack.Rd |only RAppArmor-1.0.1/RAppArmor/man/setaffinity.Rd |only RAppArmor-1.0.1/RAppArmor/man/setgid.Rd |only RAppArmor-1.0.1/RAppArmor/man/setpriority.Rd |only RAppArmor-1.0.1/RAppArmor/man/setuid.Rd |only RAppArmor-1.0.1/RAppArmor/src/aa_change_hat_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/aa_change_profile_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/aa_find_mountpoint_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/aa_getcon_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/aa_is_enabled_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/aa_revert_hat_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/getaffinity_count.c |only RAppArmor-1.0.1/RAppArmor/src/getaffinity_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/getgid_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/getpgid_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/getpriority_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/getuid_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/kill_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/ncores.c |only RAppArmor-1.0.1/RAppArmor/src/setaffinity_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/setgid_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/setpgid_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/setpriority_wrapper.c |only RAppArmor-1.0.1/RAppArmor/src/setuid_wrapper.c |only RAppArmor-1.0.1/RAppArmor/vignettes/v55i07.Rnw |only RAppArmor-1.0.1/RAppArmor/vignettes/v55i07.bib |only RAppArmor-2.0/RAppArmor/DESCRIPTION | 30 RAppArmor-2.0/RAppArmor/MD5 | 127 +-- RAppArmor-2.0/RAppArmor/NAMESPACE | 44 + RAppArmor-2.0/RAppArmor/NEWS | 19 RAppArmor-2.0/RAppArmor/R/affinity.R |only RAppArmor-2.0/RAppArmor/R/apparmor.R |only RAppArmor-2.0/RAppArmor/R/eval.secure.R | 123 ++- RAppArmor-2.0/RAppArmor/R/onAttach.R | 12 RAppArmor-2.0/RAppArmor/R/process.R |only RAppArmor-2.0/RAppArmor/R/rlimits.R | 478 +------------ RAppArmor-2.0/RAppArmor/R/unittests.R | 13 RAppArmor-2.0/RAppArmor/R/userinfo.R | 16 RAppArmor-2.0/RAppArmor/build/vignette.rds |binary RAppArmor-2.0/RAppArmor/configure | 51 + RAppArmor-2.0/RAppArmor/inst/doc/v55i07.pdf |binary RAppArmor-2.0/RAppArmor/inst/doc/v55i07.pdf.asis |only RAppArmor-2.0/RAppArmor/man/aa_change_hat.Rd | 33 RAppArmor-2.0/RAppArmor/man/aa_change_profile.Rd | 31 RAppArmor-2.0/RAppArmor/man/aa_find_mountpoint.Rd | 25 RAppArmor-2.0/RAppArmor/man/aa_getcon.Rd | 34 RAppArmor-2.0/RAppArmor/man/aa_is_enabled.Rd | 30 RAppArmor-2.0/RAppArmor/man/affinity.Rd |only RAppArmor-2.0/RAppArmor/man/eval.secure.Rd | 151 +--- RAppArmor-2.0/RAppArmor/man/process.Rd |only RAppArmor-2.0/RAppArmor/man/rlimit.Rd |only RAppArmor-2.0/RAppArmor/man/unittests.Rd | 21 RAppArmor-2.0/RAppArmor/man/userinfo.Rd | 25 RAppArmor-2.0/RAppArmor/src/Makevars.in |only RAppArmor-2.0/RAppArmor/src/affinity.c |only RAppArmor-2.0/RAppArmor/src/apparmor.c |only RAppArmor-2.0/RAppArmor/src/process.c |only RAppArmor-2.0/RAppArmor/src/rlimits.c | 255 +----- RAppArmor-2.0/RAppArmor/tests/run-all.R | 8 RAppArmor-2.0/RAppArmor/tests/testthat |only RAppArmor-2.0/RAppArmor/vignettes/v55i07.pdf.asis |only 91 files changed, 533 insertions(+), 993 deletions(-)
More information about DiversityOccupancy at CRAN
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Title: Simultaneous Variables Clustering and Regression
Description: Implements an empirical Bayes approach for simultaneous variable clustering and regression. This version also (re)implements in C++ an R script proposed by Howard Bondell that fits the Pairwise Absolute Clustering and Sparsity (PACS) methodology (see Sharma et al (2013) <DOI:10.1080/15533174.2012.707849>).
Author: Loic Yengo, Mickael Canouil
Maintainer: Loic Yengo <loic.yengo@gmail.com>
Diff between clere versions 1.1.2 dated 2015-10-08 and 1.1.3 dated 2016-03-09
clere-1.1.2/clere/inst/doc/RJpaper-vignette.ltx |only clere-1.1.2/clere/inst/doc/RJpaper-vignette.pdf |only clere-1.1.2/clere/inst/doc/Vignette.pdf |only clere-1.1.2/clere/inst/doc/Vignette.pdf.asis |only clere-1.1.2/clere/vignettes/Vignette.pdf.asis |only clere-1.1.3/clere/DESCRIPTION | 14 ++---- clere-1.1.3/clere/MD5 | 42 +++++++++++-------- clere-1.1.3/clere/NAMESPACE | 22 +++++++++ clere-1.1.3/clere/R/Clere.R | 13 +++++ clere-1.1.3/clere/build/vignette.rds |binary clere-1.1.3/clere/data/algoComp.RData |binary clere-1.1.3/clere/data/numExpRealData.RData |binary clere-1.1.3/clere/data/numExpSimData.RData |binary clere-1.1.3/clere/inst/doc/ExampleProstate.R |only clere-1.1.3/clere/inst/doc/Methods.R |only clere-1.1.3/clere/inst/doc/RealDataExample.R |only clere-1.1.3/clere/inst/doc/SEM_vs_MCEM_simulations.R |only clere-1.1.3/clere/inst/doc/SimulatedDataExample.R |only clere-1.1.3/clere/inst/doc/clere.R |only clere-1.1.3/clere/inst/doc/clere.Rnw |only clere-1.1.3/clere/inst/doc/clere.pdf |only clere-1.1.3/clere/man/algoComp.Rd | 3 - clere-1.1.3/clere/man/clere-package.Rd | 4 - clere-1.1.3/clere/man/numExpRealData.Rd | 1 clere-1.1.3/clere/man/numExpSimData.Rd | 3 - clere-1.1.3/clere/vignettes/RJournal.sty |only clere-1.1.3/clere/vignettes/biblio.bib |only clere-1.1.3/clere/vignettes/clere.Rnw |only clere-1.1.3/clere/vignettes/environ.sty |only clere-1.1.3/clere/vignettes/inconsolata.sty |only clere-1.1.3/clere/vignettes/trimspaces.sty |only clere-1.1.3/clere/vignettes/upquote.sty |only 32 files changed, 72 insertions(+), 30 deletions(-)
Title: Bayesian Fractional Polynomials
Description: Implements the Bayesian paradigm for fractional
polynomial models under the assumption of normally distributed error terms.
Author: Daniel Sabanes Bove <sabanesd@roche.com>
Maintainer: Daniel Sabanes Bove <sabanesd@roche.com>
Diff between bfp versions 0.0-27 dated 2013-12-10 and 0.0-30 dated 2016-03-09
ChangeLog | 312 +++++++++++++++++++++++++------------------------- DESCRIPTION | 23 ++- MD5 | 20 +-- NAMESPACE | 132 +++++++++++---------- R/plotCurveEstimate.R | 38 +++--- data/ozone.RData |binary src/dataStructure.cpp | 1 src/hyp2f1.c | 6 src/hyperg.cpp | 2 src/hyperg.h | 12 + src/mconf.h | 6 11 files changed, 285 insertions(+), 267 deletions(-)