Title: Easy to Use Tools for Common Forms of Random Assignment
Description: Generates random assignments for common experimental
designs: simple, complete, blocked, and clustered.
Author: Alexander Coppock [aut, cre]
Maintainer: Alexander Coppock <ac3242@columbia.edu>
Diff between randomizr versions 0.2.2 dated 2015-03-20 and 0.3.0 dated 2015-11-23
randomizr-0.2.2/randomizr/R/randomizr.r |only randomizr-0.2.2/randomizr/README.md |only randomizr-0.3.0/randomizr/DESCRIPTION | 11 randomizr-0.3.0/randomizr/MD5 | 46 + randomizr-0.3.0/randomizr/NAMESPACE | 13 randomizr-0.3.0/randomizr/R/block_and_cluster_ra.R |only randomizr-0.3.0/randomizr/R/block_ra.R |only randomizr-0.3.0/randomizr/R/cluster_ra.R |only randomizr-0.3.0/randomizr/R/complete_ra.R |only randomizr-0.3.0/randomizr/R/declare_ra.R |only randomizr-0.3.0/randomizr/R/ra_probabilities.R |only randomizr-0.3.0/randomizr/R/simple_ra.R |only randomizr-0.3.0/randomizr/build/vignette.rds |binary randomizr-0.3.0/randomizr/inst/doc/randomizr_vignette.R | 92 +-- randomizr-0.3.0/randomizr/inst/doc/randomizr_vignette.Rmd | 140 +++-- randomizr-0.3.0/randomizr/inst/doc/randomizr_vignette.html | 279 ++++++---- randomizr-0.3.0/randomizr/man/block_and_cluster_ra.Rd |only randomizr-0.3.0/randomizr/man/block_and_cluster_ra_probabilities.Rd |only randomizr-0.3.0/randomizr/man/block_ra.Rd | 29 - randomizr-0.3.0/randomizr/man/block_ra_probabilities.Rd |only randomizr-0.3.0/randomizr/man/cluster_ra.Rd | 31 - randomizr-0.3.0/randomizr/man/cluster_ra_probabilities.Rd |only randomizr-0.3.0/randomizr/man/complete_ra.Rd | 32 - randomizr-0.3.0/randomizr/man/complete_ra_probabilities.Rd |only randomizr-0.3.0/randomizr/man/conduct_ra.Rd |only randomizr-0.3.0/randomizr/man/declare_ra.Rd |only randomizr-0.3.0/randomizr/man/obtain_condition_probabilities.Rd |only randomizr-0.3.0/randomizr/man/randomizr.Rd | 2 randomizr-0.3.0/randomizr/man/simple_ra.Rd | 25 randomizr-0.3.0/randomizr/man/simple_ra_probabilities.Rd |only randomizr-0.3.0/randomizr/tests |only randomizr-0.3.0/randomizr/vignettes/randomizr_vignette.Rmd | 140 +++-- 32 files changed, 516 insertions(+), 324 deletions(-)
Title: Estimation of Diagonal Elements of Sparse Precision-Matrices
Description: Several estimators of the diagonal elements of a sparse precision
(inverse covariance) matrix from a sample of Gaussian vectors for a
given matrix of estimated marginal regression coefficients.
To install package 'gurobi', instructions at
http://user.gurobi.com/download/gurobi-optimizer and
http://www.gurobi.com/documentation/6.0/refman/r_api_overview.html.
Author: Arnak Dalalyan [aut], Samuel Balmand [aut, cre]
Maintainer: Samuel Balmand <Samuel.Balmand@ensg.eu>
Diff between DESP versions 0.1-5 dated 2015-11-20 and 0.1-6 dated 2015-11-23
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/DESP-package.Rd | 4 ++-- src/scsSRL_B.c | 13 +++++++++---- src/scsSolveSOCP.c | 2 +- 6 files changed, 26 insertions(+), 16 deletions(-)
Title: D3 Javascript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between scatterD3 versions 0.3 dated 2015-10-26 and 0.4 dated 2015-11-23
DESCRIPTION | 10 +- MD5 | 19 ++--- NEWS | 9 ++ R/scatterD3.R | 14 +++ inst/doc/introduction.Rmd | 8 +- inst/doc/introduction.html | 46 ++++++------ inst/htmlwidgets/scatterD3.js | 153 +++++++++++++++++++++++++++--------------- man/clean_var_levels.Rd |only man/scatterD3-shiny.Rd | 2 man/scatterD3.Rd | 1 vignettes/introduction.Rmd | 8 +- 11 files changed, 168 insertions(+), 102 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 1.2-2 dated 2015-11-18 and 1.2-3 dated 2015-11-23
DESCRIPTION | 8 ++-- MD5 | 74 ++++++++++++++++++++--------------------- R/jomo1cat.MCMCchain.R | 2 + R/jomo1cat.R | 2 + R/jomo1con.MCMCchain.R | 2 + R/jomo1con.R | 2 + R/jomo1mix.MCMCchain.R | 3 + R/jomo1mix.R | 3 + R/jomo1rancat.MCMCchain.R | 8 ++++ R/jomo1rancat.R | 8 ++++ R/jomo1rancathr.MCMCchain.R | 8 ++++ R/jomo1rancathr.R | 8 ++++ R/jomo1rancon.MCMCchain.R | 8 ++++ R/jomo1rancon.R | 8 ++++ R/jomo1ranconhr.MCMCchain.R | 8 ++++ R/jomo1ranconhr.R | 8 ++++ R/jomo1ranmix.MCMCchain.R | 9 ++++ R/jomo1ranmix.R | 9 ++++ R/jomo1ranmixhr.MCMCchain.R | 9 ++++ R/jomo1ranmixhr.R | 9 ++++ man/jomo1cat.MCMCchain.Rd | 2 - man/jomo1cat.Rd | 2 - man/jomo1mix.MCMCchain.Rd | 2 - man/jomo1mix.Rd | 2 - man/jomo1ran.MCMCchain.Rd | 2 - man/jomo1ran.Rd | 2 - man/jomo1rancat.MCMCchain.Rd | 4 +- man/jomo1rancat.Rd | 4 +- man/jomo1rancathr.MCMCchain.Rd | 4 +- man/jomo1rancathr.Rd | 4 +- man/jomo1rancon.MCMCchain.Rd | 2 - man/jomo1rancon.Rd | 2 - man/jomo1ranconhr.MCMCchain.Rd | 2 - man/jomo1ranconhr.Rd | 2 - man/jomo1ranmix.MCMCchain.Rd | 4 +- man/jomo1ranmix.Rd | 4 +- man/jomo1ranmixhr.MCMCchain.Rd | 4 +- man/jomo1ranmixhr.Rd | 4 +- 38 files changed, 181 insertions(+), 67 deletions(-)
Title: Flexible Parametric Models for Censored and Truncated Data
Description: Estimation of flexible parametric models for survival data.
Author: Paolo Frumento <paolo.frumento@ki.se>
Maintainer: Paolo Frumento <paolo.frumento@ki.se>
Diff between flexPM versions 1.0 dated 2015-06-08 and 2.0 dated 2015-11-23
DESCRIPTION | 10 MD5 | 12 NAMESPACE | 34 ++ R/flexPM.R | 621 ++++++++++++++++++++++++------------------------- man/flexPM-internal.Rd | 19 - man/flexPM.Rd | 109 ++++---- man/predict.flexPM.Rd | 7 7 files changed, 420 insertions(+), 392 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, Luca Scrucca, Yuan Tang, and Can Candan.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>
Diff between caret versions 6.0-58 dated 2015-10-22 and 6.0-62 dated 2015-11-23
DESCRIPTION | 10 ++++----- MD5 | 52 ++++++++++++++++++++++++----------------------- NAMESPACE | 2 + R/adaptive.R | 47 ++++++++++++++++++++++++++++-------------- R/avNNet.R | 8 ++++++- R/ggplot.R | 8 +++---- R/learning_curve.R |only R/misc.R | 2 - R/plot.varImp.train.R | 34 ++++++++++++++++++++++++++++++ R/print.train.R | 1 R/train.default.R | 9 +++++++- inst/NEWS.Rd | 17 +++++++++++++++ inst/models/models.RData |binary man/avNNet.Rd | 5 +++- man/confusionMatrix.Rd | 2 - man/extractPrediction.Rd | 2 - man/ga_functions.Rd | 2 - man/gafs.default.Rd | 6 +++-- man/learning_curve.Rd |only man/models.Rd | 37 +++++++++++++++++++++++++++++++++ man/plot.rfe.Rd | 9 ++++---- man/plot.train.Rd | 9 +++++--- man/plot.varImp.train.Rd | 11 +++++++-- man/preProcess.Rd | 2 - man/safs.default.Rd | 4 ++- man/sensitivity.Rd | 2 - man/train.Rd | 2 - man/trainControl.Rd | 4 ++- 28 files changed, 213 insertions(+), 74 deletions(-)
Title: Tools for Antitrust Practitioners
Description: A collection of tools for antitrust practitioners, including the ability to calibrate different consumer demand systems and simulate the effects mergers under different competitive regimes.
Author: Charles Taragin and Michael Sandfort
Maintainer: Charles Taragin <charles.taragin@usdoj.gov>
Diff between antitrust versions 0.95 dated 2015-11-19 and 0.95.1 dated 2015-11-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/manual.Rnw | 2 +- inst/doc/manual.pdf |binary vignettes/manual.Rnw | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: The Residual-Based Predictiveness Curve
Description: The RBP curve is a visual tool to assess the
performance of prediction models.
Author: Giuseppe Casalicchio, Bernd Bischl
Maintainer: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>
Diff between RBPcurve versions 1.0-20 dated 2015-01-09 and 1.0-33 dated 2015-11-23
RBPcurve-1.0-20/RBPcurve/README.md |only RBPcurve-1.0-33/RBPcurve/DESCRIPTION | 17 ++--- RBPcurve-1.0-33/RBPcurve/MD5 | 31 ++++------ RBPcurve-1.0-33/RBPcurve/NAMESPACE | 11 +++ RBPcurve-1.0-33/RBPcurve/R/addGoodCalib.R | 2 RBPcurve-1.0-33/RBPcurve/R/addPrevalence.R | 5 - RBPcurve-1.0-33/RBPcurve/R/addRates.R | 20 ++++-- RBPcurve-1.0-33/RBPcurve/R/addWellCalib.R | 80 +++++++++++++++++--------- RBPcurve-1.0-33/RBPcurve/R/plotRBPCurve.R | 29 ++++++--- RBPcurve-1.0-33/RBPcurve/R/zzz.R | 2 RBPcurve-1.0-33/RBPcurve/man/addGoodCalib.Rd | 6 - RBPcurve-1.0-33/RBPcurve/man/addPEV.Rd | 2 RBPcurve-1.0-33/RBPcurve/man/addPrevalence.Rd | 9 ++ RBPcurve-1.0-33/RBPcurve/man/addRates.Rd | 23 +++++-- RBPcurve-1.0-33/RBPcurve/man/addWellCalib.Rd | 23 ++++--- RBPcurve-1.0-33/RBPcurve/man/makeRBPObj.Rd | 6 - RBPcurve-1.0-33/RBPcurve/man/plotRBPCurve.Rd | 21 ++++-- 17 files changed, 188 insertions(+), 99 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-16 0.7.3
2015-07-04 0.6.1
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre]
Maintainer: Jonathan Bartlett <jonathan.bartlett@lshtm.ac.uk>
Diff between smcfcs versions 1.1.0 dated 2015-08-21 and 1.1.1 dated 2015-11-23
DESCRIPTION | 7 ++++--- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/smcfcs.r | 15 +++++++++++---- README.md | 6 ++++++ man/ex_compet.Rd | 2 +- man/ex_coxquad.Rd | 2 +- man/ex_lininter.Rd | 2 +- man/ex_linquad.Rd | 2 +- man/ex_logisticquad.Rd | 2 +- man/smcfcs.Rd | 4 ++-- vignettes/smcfcs-vignette.Rmd | 2 +- 12 files changed, 41 insertions(+), 27 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended
for people coming from other statistical software packages like 'SPSS', and/
or who are new to R), supporting following common tasks: 1) Reading and writing
data between R and other statistical software packages like 'SPSS', 'SAS' or
'Stata' and working with labelled data; this includes easy ways to get and set
label attributes, to convert labelled vectors into factors (and vice versa),
or to deal with multiple declared missing values etc. 2) Data transformation
tasks like recoding, dichotomizing or grouping variables, setting and replacing
missing values. 3) Convenient functions to perform frequently used statistical
tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.2 dated 2015-10-12 and 1.3 dated 2015-11-23
sjmisc-1.2/sjmisc/man/to_sjPlot.Rd |only sjmisc-1.3/sjmisc/DESCRIPTION | 29 - sjmisc-1.3/sjmisc/MD5 | 210 +++---- sjmisc-1.3/sjmisc/NAMESPACE | 231 ++++---- sjmisc-1.3/sjmisc/NEWS | 18 sjmisc-1.3/sjmisc/R/add_labels.R | 62 +- sjmisc-1.3/sjmisc/R/as_labelled.R | 3 sjmisc-1.3/sjmisc/R/copy_labels.R | 4 sjmisc-1.3/sjmisc/R/cronb.R | 2 sjmisc-1.3/sjmisc/R/dicho.R | 25 sjmisc-1.3/sjmisc/R/fill_labels.R | 11 sjmisc-1.3/sjmisc/R/get_label.R | 233 ++++---- sjmisc-1.3/sjmisc/R/get_labels.R | 517 +++++++++--------- sjmisc-1.3/sjmisc/R/get_values.R | 2 sjmisc-1.3/sjmisc/R/group_var.R | 52 - sjmisc-1.3/sjmisc/R/helpfunctions.R | 263 ++++----- sjmisc-1.3/sjmisc/R/is_even.R | 3 sjmisc-1.3/sjmisc/R/is_odd.R | 3 sjmisc-1.3/sjmisc/R/labelled.R | 6 sjmisc-1.3/sjmisc/R/mic.R | 12 sjmisc-1.3/sjmisc/R/rec.R | 38 + sjmisc-1.3/sjmisc/R/ref_lvl.R |only sjmisc-1.3/sjmisc/R/reliab_test.R | 11 sjmisc-1.3/sjmisc/R/remove_all_labels.R |only sjmisc-1.3/sjmisc/R/remove_labels.R | 126 +++- sjmisc-1.3/sjmisc/R/replace_na.R | 136 +++- sjmisc-1.3/sjmisc/R/se.R | 182 +++--- sjmisc-1.3/sjmisc/R/set_label.R | 346 ++++++------ sjmisc-1.3/sjmisc/R/set_labels.R | 805 +++++++++++++++-------------- sjmisc-1.3/sjmisc/R/set_na.R | 46 + sjmisc-1.3/sjmisc/R/split_var.R |only sjmisc-1.3/sjmisc/R/to_factor.R | 271 +++++---- sjmisc-1.3/sjmisc/R/to_label.R | 2 sjmisc-1.3/sjmisc/R/to_value.R | 8 sjmisc-1.3/sjmisc/R/trim.R | 3 sjmisc-1.3/sjmisc/R/unlabel.R | 123 ++-- sjmisc-1.3/sjmisc/R/word_wrap.R | 123 ++-- sjmisc-1.3/sjmisc/R/zap_labels.R | 6 sjmisc-1.3/sjmisc/README.md | 19 sjmisc-1.3/sjmisc/man/add_labels.Rd | 38 - sjmisc-1.3/sjmisc/man/as_labelled.Rd | 7 sjmisc-1.3/sjmisc/man/chisq_gof.Rd | 3 sjmisc-1.3/sjmisc/man/cod.Rd | 3 sjmisc-1.3/sjmisc/man/converge_ok.Rd | 105 +-- sjmisc-1.3/sjmisc/man/copy_labels.Rd | 5 sjmisc-1.3/sjmisc/man/cramer.Rd | 7 sjmisc-1.3/sjmisc/man/cronb.Rd | 4 sjmisc-1.3/sjmisc/man/cv.Rd | 3 sjmisc-1.3/sjmisc/man/dicho.Rd | 11 sjmisc-1.3/sjmisc/man/efc.Rd | 3 sjmisc-1.3/sjmisc/man/eta_sq.Rd | 3 sjmisc-1.3/sjmisc/man/fill_labels.Rd | 5 sjmisc-1.3/sjmisc/man/frq.Rd | 3 sjmisc-1.3/sjmisc/man/get_label.Rd | 154 ++--- sjmisc-1.3/sjmisc/man/get_labels.Rd | 322 +++++------ sjmisc-1.3/sjmisc/man/get_na.Rd | 3 sjmisc-1.3/sjmisc/man/get_na_flags.Rd | 3 sjmisc-1.3/sjmisc/man/get_values.Rd | 4 sjmisc-1.3/sjmisc/man/group_labels.Rd | 10 sjmisc-1.3/sjmisc/man/group_str.Rd | 5 sjmisc-1.3/sjmisc/man/group_var.Rd | 25 sjmisc-1.3/sjmisc/man/hoslem_gof.Rd | 3 sjmisc-1.3/sjmisc/man/icc.Rd | 3 sjmisc-1.3/sjmisc/man/is_crossed.Rd | 3 sjmisc-1.3/sjmisc/man/is_empty.Rd | 3 sjmisc-1.3/sjmisc/man/is_even.Rd | 6 sjmisc-1.3/sjmisc/man/is_labelled.Rd | 2 sjmisc-1.3/sjmisc/man/is_nested.Rd | 3 sjmisc-1.3/sjmisc/man/is_num_fac.Rd | 3 sjmisc-1.3/sjmisc/man/is_odd.Rd | 6 sjmisc-1.3/sjmisc/man/labelled.Rd | 11 sjmisc-1.3/sjmisc/man/levene_test.Rd | 3 sjmisc-1.3/sjmisc/man/mean_n.Rd | 5 sjmisc-1.3/sjmisc/man/mic.Rd | 17 sjmisc-1.3/sjmisc/man/mwu.Rd | 3 sjmisc-1.3/sjmisc/man/phi.Rd | 7 sjmisc-1.3/sjmisc/man/pseudo_r2.Rd | 3 sjmisc-1.3/sjmisc/man/read_sas.Rd | 2 sjmisc-1.3/sjmisc/man/read_spss.Rd | 3 sjmisc-1.3/sjmisc/man/read_stata.Rd | 2 sjmisc-1.3/sjmisc/man/rec.Rd | 17 sjmisc-1.3/sjmisc/man/recode_to.Rd | 3 sjmisc-1.3/sjmisc/man/ref_lvl.Rd |only sjmisc-1.3/sjmisc/man/reliab_test.Rd | 7 sjmisc-1.3/sjmisc/man/remove_all_labels.Rd |only sjmisc-1.3/sjmisc/man/remove_labels.Rd | 44 + sjmisc-1.3/sjmisc/man/replace_na.Rd | 11 sjmisc-1.3/sjmisc/man/rmse.Rd | 3 sjmisc-1.3/sjmisc/man/se.Rd | 6 sjmisc-1.3/sjmisc/man/set_label.Rd | 220 ++++--- sjmisc-1.3/sjmisc/man/set_labels.Rd | 280 +++++----- sjmisc-1.3/sjmisc/man/set_na.Rd | 28 - sjmisc-1.3/sjmisc/man/sjmisc-package.Rd | 4 sjmisc-1.3/sjmisc/man/split_var.Rd |only sjmisc-1.3/sjmisc/man/std_beta.Rd | 3 sjmisc-1.3/sjmisc/man/str_pos.Rd | 5 sjmisc-1.3/sjmisc/man/table_values.Rd | 3 sjmisc-1.3/sjmisc/man/to_factor.Rd | 191 +++--- sjmisc-1.3/sjmisc/man/to_label.Rd | 3 sjmisc-1.3/sjmisc/man/to_na.Rd | 3 sjmisc-1.3/sjmisc/man/to_value.Rd | 7 sjmisc-1.3/sjmisc/man/trim.Rd | 8 sjmisc-1.3/sjmisc/man/unlabel.Rd |only sjmisc-1.3/sjmisc/man/weight.Rd | 7 sjmisc-1.3/sjmisc/man/weight2.Rd | 3 sjmisc-1.3/sjmisc/man/word_wrap.Rd | 6 sjmisc-1.3/sjmisc/man/write_spss.Rd | 4 sjmisc-1.3/sjmisc/man/write_stata.Rd | 4 sjmisc-1.3/sjmisc/man/zap_labels.Rd | 7 sjmisc-1.3/sjmisc/man/zap_unlabelled.Rd | 7 110 files changed, 3029 insertions(+), 2600 deletions(-)
Title: Nonparametric Simulation of RNA-Seq Data
Description: RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method. We develop a data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source RNA-seq dataset provided by the user. Users control the proportion of genes simulated to be differentially expressed (DE) and can provide a vector of weights to control the distribution of effect sizes. The algorithm requires a matrix of RNA-seq read counts with large sample sizes in at least two treatment groups. Many datasets are available that fit this standard.
Author: Samuel Benidt
Maintainer: Samuel Benidt <sgbenidt@gmail.com>
Diff between SimSeq versions 1.3.0 dated 2015-03-07 and 1.4.0 dated 2015-11-23
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 4 +++- NEWS | 3 +++ R/SimData.R | 2 +- inst/CITATION | 4 +++- man/CalcPvalWilcox.Rd | 2 +- man/SimData.Rd | 10 +++++----- man/SimSeq-package.Rd | 6 +++--- man/SortData.Rd | 2 +- man/kidney.Rd | 6 +++--- 11 files changed, 38 insertions(+), 31 deletions(-)
Title: Quantile Universal Threshold
Description: Selection of a threshold parameter for GLM-lasso to obtain a sparse model
with a good compromise between high true positive rate and low false discovery rate.
Author: Jairo Diaz, Sylvain Sardy, Caroline Giacobino, Nick Hengartner.
Maintainer: Jairo Diaz <jairo.diaz@unige.ch>
Diff between qut versions 1.0 dated 2015-09-20 and 1.0.1 dated 2015-11-23
DESCRIPTION | 6 - MD5 | 15 ++-- NAMESPACE | 5 - R/coef.qut.R |only R/lambdaqut.R | 30 ++++---- R/qut.R | 198 +++++++++++++++++++++++++++++++---------------------- man/lambdaqut.Rd | 6 + man/predict.qut.Rd | 8 +- man/qut.Rd | 15 ++-- 9 files changed, 168 insertions(+), 115 deletions(-)
Title: Parametric Network Enrichment Analysis
Description: Includes functions and examples for Parametric Network Enrichment Analysis.
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Diff between pnea versions 1.1.1 dated 2015-09-30 and 1.2.0 dated 2015-11-23
pnea-1.1.1/pnea/build |only pnea-1.2.0/pnea/DESCRIPTION | 10 - pnea-1.2.0/pnea/MD5 | 22 +-- pnea-1.2.0/pnea/NAMESPACE | 1 pnea-1.2.0/pnea/R/pnea.R | 260 +++++++++++++++++++++++------------- pnea-1.2.0/pnea/data/yeast.RData |binary pnea-1.2.0/pnea/man/netfromadj.Rd |only pnea-1.2.0/pnea/man/plot.pnea.Rd | 11 - pnea-1.2.0/pnea/man/pnea-package.Rd | 4 pnea-1.2.0/pnea/man/pnea.Rd | 92 ++++++------ pnea-1.2.0/pnea/man/print.pnea.Rd | 6 pnea-1.2.0/pnea/man/summary.pnea.Rd | 11 - pnea-1.2.0/pnea/man/yeast.Rd | 6 13 files changed, 249 insertions(+), 174 deletions(-)
Title: An R Pandoc Writer
Description: Contains some functions catching all messages, stdout and other
useful information while evaluating R code and other helpers to return user
specified text elements (like: header, paragraph, table, image, lists etc.)
in pandoc's markdown or several type of R objects similarly automatically
transformed to markdown format. Also capable of exporting/converting (the
resulting) complex pandoc documents to e.g. HTML, PDF, docx or odt. This
latter reporting feature is supported in brew syntax or with a custom
reference class with a smarty caching backend.
Author: Gergely Daróczi <daroczig@rapporter.net>, Roman Tsegelskyi
<roman.tsegelskyi@gmail.com>
Maintainer: Gergely Daróczi <daroczig@rapporter.net>
Diff between pander versions 0.5.2 dated 2015-05-18 and 0.6.0 dated 2015-11-23
pander-0.5.2/pander/man/pander.option.Rd |only pander-0.5.2/pander/man/pander.return.Rd |only pander-0.6.0/pander/DESCRIPTION | 19 pander-0.6.0/pander/MD5 | 286 +- pander-0.6.0/pander/NAMESPACE | 62 pander-0.6.0/pander/NEWS | 73 pander-0.6.0/pander/R/R5.R | 42 pander-0.6.0/pander/R/S3.R | 1466 +++++++++++---- pander-0.6.0/pander/R/brew.R | 182 + pander-0.6.0/pander/R/convert.R | 76 pander-0.6.0/pander/R/ess-functions.R | 11 pander-0.6.0/pander/R/evals.R | 784 +++++--- pander-0.6.0/pander/R/graph.R | 93 pander-0.6.0/pander/R/helpers.R | 232 +- pander-0.6.0/pander/R/options.R | 74 pander-0.6.0/pander/R/pandoc.R | 714 ++++--- pander-0.6.0/pander/README.md | 230 +- pander-0.6.0/pander/build |only pander-0.6.0/pander/inst/README.brew | 152 + pander-0.6.0/pander/inst/doc |only pander-0.6.0/pander/inst/tests/test-S3.R | 956 ++++++++- pander-0.6.0/pander/inst/tests/test-brew.R | 49 pander-0.6.0/pander/inst/tests/test-convert.R |only pander-0.6.0/pander/inst/tests/test-evals.R | 336 ++- pander-0.6.0/pander/inst/tests/test-helpers.R | 87 pander-0.6.0/pander/inst/tests/test-missing.R | 16 pander-0.6.0/pander/man/Pandoc-class.Rd | 2 pander-0.6.0/pander/man/Pandoc.brew.Rd | 2 pander-0.6.0/pander/man/Pandoc.convert.Rd | 4 pander-0.6.0/pander/man/add.blank.lines.Rd | 2 pander-0.6.0/pander/man/add.lattice.grid.Rd | 2 pander-0.6.0/pander/man/add.lattice.xsubticks.Rd | 2 pander-0.6.0/pander/man/add.minor.ticks.Rd | 2 pander-0.6.0/pander/man/add.significance.stars.Rd | 2 pander-0.6.0/pander/man/brew.Rd | 2 pander-0.6.0/pander/man/cache.off.Rd | 2 pander-0.6.0/pander/man/check_caption.Rd | 2 pander-0.6.0/pander/man/check_digits.Rd |only pander-0.6.0/pander/man/coef_mat.Rd |only pander-0.6.0/pander/man/emphasize.rows.Rd | 20 pander-0.6.0/pander/man/eval.msgs.Rd | 4 pander-0.6.0/pander/man/evals.Rd | 74 pander-0.6.0/pander/man/evalsOptions.Rd | 11 pander-0.6.0/pander/man/get.alignment.Rd | 2 pander-0.6.0/pander/man/get.caption.Rd | 2 pander-0.6.0/pander/man/get.emphasize.Rd | 2 pander-0.6.0/pander/man/get.storage.Rd | 2 pander-0.6.0/pander/man/has.rownames.Rd | 2 pander-0.6.0/pander/man/multitable.Rd |only pander-0.6.0/pander/man/openFileInOS.Rd | 2 pander-0.6.0/pander/man/p.Rd | 31 pander-0.6.0/pander/man/pander.Arima.Rd |only pander-0.6.0/pander/man/pander.CrossTable.Rd | 9 pander-0.6.0/pander/man/pander.Date.Rd | 2 pander-0.6.0/pander/man/pander.NULL.Rd | 2 pander-0.6.0/pander/man/pander.POSIXct.Rd | 2 pander-0.6.0/pander/man/pander.POSIXlt.Rd | 2 pander-0.6.0/pander/man/pander.Rd | 3 pander-0.6.0/pander/man/pander.anova.Rd | 7 pander-0.6.0/pander/man/pander.aov.Rd | 2 pander-0.6.0/pander/man/pander.aovlist.Rd | 2 pander-0.6.0/pander/man/pander.call.Rd | 2 pander-0.6.0/pander/man/pander.cast_df.Rd | 2 pander-0.6.0/pander/man/pander.character.Rd | 2 pander-0.6.0/pander/man/pander.clogit.Rd | 2 pander-0.6.0/pander/man/pander.coxph.Rd | 2 pander-0.6.0/pander/man/pander.cph.Rd |only pander-0.6.0/pander/man/pander.data.frame.Rd | 2 pander-0.6.0/pander/man/pander.default.Rd | 2 pander-0.6.0/pander/man/pander.density.Rd | 2 pander-0.6.0/pander/man/pander.describe.Rd | 10 pander-0.6.0/pander/man/pander.evals.Rd | 2 pander-0.6.0/pander/man/pander.factor.Rd | 2 pander-0.6.0/pander/man/pander.formula.Rd | 2 pander-0.6.0/pander/man/pander.ftable.Rd | 2 pander-0.6.0/pander/man/pander.function.Rd | 2 pander-0.6.0/pander/man/pander.glm.Rd | 2 pander-0.6.0/pander/man/pander.glm.rms.Rd |only pander-0.6.0/pander/man/pander.gtable.Rd |only pander-0.6.0/pander/man/pander.htest.Rd | 2 pander-0.6.0/pander/man/pander.image.Rd | 2 pander-0.6.0/pander/man/pander.irts.Rd |only pander-0.6.0/pander/man/pander.list.Rd | 2 pander-0.6.0/pander/man/pander.lm.Rd | 6 pander-0.6.0/pander/man/pander.lme.Rd | 6 pander-0.6.0/pander/man/pander.logical.Rd | 2 pander-0.6.0/pander/man/pander.lrm.Rd |only pander-0.6.0/pander/man/pander.manova.Rd |only pander-0.6.0/pander/man/pander.matrix.Rd | 2 pander-0.6.0/pander/man/pander.microbenchmark.Rd | 4 pander-0.6.0/pander/man/pander.mtable.Rd | 2 pander-0.6.0/pander/man/pander.name.Rd |only pander-0.6.0/pander/man/pander.nls.Rd |only pander-0.6.0/pander/man/pander.numeric.Rd | 2 pander-0.6.0/pander/man/pander.ols.Rd |only pander-0.6.0/pander/man/pander.orm.Rd |only pander-0.6.0/pander/man/pander.polr.Rd |only pander-0.6.0/pander/man/pander.prcomp.Rd | 2 pander-0.6.0/pander/man/pander.randomForest.Rd |only pander-0.6.0/pander/man/pander.rapport.Rd | 2 pander-0.6.0/pander/man/pander.rlm.Rd | 2 pander-0.6.0/pander/man/pander.sessionInfo.Rd | 2 pander-0.6.0/pander/man/pander.smooth.spline.Rd | 2 pander-0.6.0/pander/man/pander.stat.table.Rd | 2 pander-0.6.0/pander/man/pander.summary.aov.Rd | 2 pander-0.6.0/pander/man/pander.summary.aovlist.Rd | 2 pander-0.6.0/pander/man/pander.summary.glm.Rd | 2 pander-0.6.0/pander/man/pander.summary.lm.Rd | 2 pander-0.6.0/pander/man/pander.summary.lme.Rd |only pander-0.6.0/pander/man/pander.summary.manova.Rd |only pander-0.6.0/pander/man/pander.summary.nls.Rd |only pander-0.6.0/pander/man/pander.summary.polr.Rd |only pander-0.6.0/pander/man/pander.summary.prcomp.Rd | 2 pander-0.6.0/pander/man/pander.summary.rms.Rd |only pander-0.6.0/pander/man/pander.summary.survreg.Rd |only pander-0.6.0/pander/man/pander.summary.table.Rd |only pander-0.6.0/pander/man/pander.survdiff.Rd | 2 pander-0.6.0/pander/man/pander.survfit.Rd | 4 pander-0.6.0/pander/man/pander.survreg.Rd |only pander-0.6.0/pander/man/pander.table.Rd | 2 pander-0.6.0/pander/man/pander.tabular.Rd | 20 pander-0.6.0/pander/man/pander.ts.Rd | 2 pander-0.6.0/pander/man/pander.vector.Rd | 2 pander-0.6.0/pander/man/pander.zoo.Rd | 2 pander-0.6.0/pander/man/panderOptions.Rd | 11 pander-0.6.0/pander/man/pander_return.Rd | 2 pander-0.6.0/pander/man/pandoc.date.return.Rd | 2 pander-0.6.0/pander/man/pandoc.emphasis.return.Rd | 2 pander-0.6.0/pander/man/pandoc.footnote.return.Rd | 2 pander-0.6.0/pander/man/pandoc.formula.return.Rd | 4 pander-0.6.0/pander/man/pandoc.header.return.Rd | 2 pander-0.6.0/pander/man/pandoc.horizontal.rule.return.Rd | 2 pander-0.6.0/pander/man/pandoc.image.return.Rd | 2 pander-0.6.0/pander/man/pandoc.indent.Rd | 2 pander-0.6.0/pander/man/pandoc.link.return.Rd | 2 pander-0.6.0/pander/man/pandoc.list.return.Rd | 2 pander-0.6.0/pander/man/pandoc.p.return.Rd | 2 pander-0.6.0/pander/man/pandoc.strikeout.return.Rd | 2 pander-0.6.0/pander/man/pandoc.strong.return.Rd | 2 pander-0.6.0/pander/man/pandoc.table.return.Rd | 47 pander-0.6.0/pander/man/pandoc.title.return.Rd | 2 pander-0.6.0/pander/man/pandoc.verbatim.return.Rd | 2 pander-0.6.0/pander/man/redraw.recordedplot.Rd | 2 pander-0.6.0/pander/man/redrawPlot.Rd | 8 pander-0.6.0/pander/man/remove.extra.newlines.Rd | 2 pander-0.6.0/pander/man/repChar.Rd | 2 pander-0.6.0/pander/man/set.alignment.Rd | 2 pander-0.6.0/pander/man/set.caption.Rd | 2 pander-0.6.0/pander/man/splitLine.Rd | 8 pander-0.6.0/pander/man/trim.spaces.Rd | 2 pander-0.6.0/pander/man/wrap.Rd | 6 pander-0.6.0/pander/vignettes |only 152 files changed, 4458 insertions(+), 1939 deletions(-)
Title: Kaplan-Meier Estimator with Constraints for Right Censored Data
-- a Recursive Computational Algorithm
Description: Linearly constrained Kaplan-Meier estimator for right censored data. This version does empirical likelihood ratio test with right censored data with linear type constraint and hypothesis testing for coefficients in accelerated failure time model.
Author: Yifan Yang [aut,cre], Mai Zhou [aut]
Maintainer: Yifan Yang <yifan.yang@uky.edu>
Diff between kmc versions 0.1-2 dated 2013-12-25 and 0.2-2 dated 2015-11-23
DESCRIPTION | 20 +++--- MD5 | 25 ++++---- NAMESPACE | 7 +- R/RcppExport.R | 30 +++++++++ R/kmc.R | 106 ++++++++++++++++++++++++++++++---- inst |only man/kmc.bjtest.Rd |only man/kmc.solve.Rd | 25 +++----- man/plotkmc.Rd | 27 +++----- man/print.kmcS3.Rd | 25 ++------ src/Makevars.win | 6 - src/RcppExport.cpp | 17 +++++ src/common.h |only src/common_kmc.h |only src/kmc.cpp | 161 ++++++++++++++++++++++++++++++++++++++++++----------- src/surv2.c |only 16 files changed, 335 insertions(+), 114 deletions(-)
Title: Probabilities for Pedigrees Given DNA Data
Description:
An interface to the core Familias functions (www.familias.name),
which are programmed in C++.
Author: Petter Mostad, Thore Egeland, Ivar Simonsson
Maintainer: Petter Mostad <mostad@chalmers.se>
Diff between Familias versions 2.2 dated 2015-03-09 and 2.3 dated 2015-11-23
DESCRIPTION | 12 +- MD5 | 24 ++-- NAMESPACE | 2 R/ConvertPed.R | 4 R/FamiliasLocus.R | 204 +++++++++++++++++++++++++++++++++--------- R/FamiliasPedigree.R | 16 +-- R/FamiliasPosterior.R | 40 ++++---- R/FamiliasPrior.R | 26 ++--- R/plot.FamiliasPedigree.R | 2 data/NorwegianFrequencies.rda |binary man/Familias-package.Rd | 6 - man/FamiliasLocus.Rd | 65 +++++++------ man/FamiliasPosterior.Rd | 30 +++--- 13 files changed, 280 insertions(+), 151 deletions(-)
More information about ForecastCombinations at CRAN
Permanent link
Title: Directional Statistics
Description: A collection of R functions for directional data analysis.
Author: Michail Tsagris, Giorgos Athineou
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 1.0 dated 2015-11-12 and 1.5 dated 2015-11-23
DESCRIPTION | 6 ++-- MD5 | 56 ++++++++++++++++++++++----------------------- R/spml.reg.R | 17 ++++++++----- man/Arotation.Rd | 6 ++-- man/Directional-package.Rd | 2 - man/f.rbing.Rd | 5 +--- man/fb.saddle.Rd | 2 - man/kent.datacontour.Rd | 4 +-- man/kent.mle.Rd | 6 ++-- man/meandir.test.Rd | 4 +-- man/mix.vmf.Rd | 10 ++++---- man/mixvmf.contour.Rd | 14 +++++------ man/rayleigh.Rd | 4 +-- man/rbingham.Rd | 4 +-- man/rfb.Rd | 22 ++++++++--------- man/rmixvmf.Rd | 10 ++++---- man/rot.matrix.Rd | 6 ++-- man/rotation.Rd | 10 ++++---- man/rvmf.Rd | 4 +-- man/spher.reg.Rd | 28 +++++++++++----------- man/spherconc.tet.Rd | 4 +-- man/spml.reg.Rd | 10 ++++++-- man/vm.kde.Rd | 10 ++++---- man/vmf.da.Rd | 4 +-- man/vmf.kde.Rd | 8 +++--- man/vmf.kerncontour.Rd | 6 ++-- man/vmfkde.tune.Rd | 3 -- man/vmfkde.tune_2.Rd | 3 -- man/vmkde.tune_2.Rd | 2 - 29 files changed, 139 insertions(+), 131 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Description: Nested block designs for unstructured treatment sets where
blocks can be repeatedly nested and treatments can have different levels of
replication. Blocks are optimized hierarchically from the top down with each
set of nested blocks optimized within the levels of any existing higher-level
blocks. Block sizes are equal if the number of blocks exactly divides the number
of plots, otherwise they differ by at most one plot. The design output is a
data table giving a randomised allocation of treatments to blocks together with
a plan table showing treatments in blocks and a set of blocks-by-treatments
incidence matrices, one for each blocks stratum.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 1.8 dated 2015-10-11 and 1.9 dated 2015-11-23
blocksdesign-1.8/blocksdesign/R/pairwise_effics.r |only blocksdesign-1.8/blocksdesign/man/efficiencies.Rd |only blocksdesign-1.9/blocksdesign/DESCRIPTION | 23 blocksdesign-1.9/blocksdesign/MD5 | 18 blocksdesign-1.9/blocksdesign/NAMESPACE | 3 blocksdesign-1.9/blocksdesign/R/blocks.r | 458 ++++++-------- blocksdesign-1.9/blocksdesign/R/blocksdesign-package.r | 52 - blocksdesign-1.9/blocksdesign/R/upper_bounds.r | 109 +-- blocksdesign-1.9/blocksdesign/man/blocks.Rd | 79 +- blocksdesign-1.9/blocksdesign/man/blocksdesign-package.Rd | 62 - blocksdesign-1.9/blocksdesign/man/upper_bounds.Rd | 22 11 files changed, 393 insertions(+), 433 deletions(-)
Title: Aggregate Numeric, Date and Categorical Variables by an ID
Description: Convenience functions for aggregating data frame. Currently mean, sum and variance are supported. For Date variables, recency and duration are supported. There is also support for dummy variables in predictive contexts.
Author: Matthias Bogaert, Michel Ballings, Dirk Van den Poel
Maintainer: Matthias Bogaert <matthias.bogaert@ugent.be>
Diff between AggregateR versions 0.0.1 dated 2015-10-01 and 0.0.2 dated 2015-11-23
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NAMESPACE | 2 +- R/Aggregate.R | 53 +++++++++++++++++++++++++++++++++++++++++------------ inst/NEWS | 4 ++++ man/Aggregate.Rd | 14 ++++++++++---- 6 files changed, 68 insertions(+), 29 deletions(-)