Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing
and/or imputed values are introduced, which can be used for exploring the data and the
structure of the missing and/or imputed values. Depending on this structure
of the missing values, the corresponding methods may help to identify the
mechanism generating the missing values and allows to explore the data
including missing values. In addition, the quality of imputation can be
visually explored using various univariate, bivariate, multiple and
multivariate plot methods. A graphical user interface available in the
separate package VIMGUI allows an easy handling of the implemented plot
methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik, Bernd Prantner
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 4.4.1 dated 2015-09-15 and 4.5.0 dated 2016-06-29
DESCRIPTION | 33 +- MD5 | 104 +++--- NAMESPACE | 241 +++++++------- NEWS | 57 +-- R/VIM-package.R | 2 R/gower.dist.R | 134 ++++---- R/hotdeck.R | 2 R/kNNFaster.R | 746 ++++++++++++++++++++++++---------------------- data/SBS5242.rda |binary data/chorizonDL.rda |binary data/kola.background.rda |binary data/sleep.rda |binary data/tao.rda |binary data/testdata.RData |binary man/SBS5242.Rd | 58 +-- man/VIM-package.Rd | 104 +++--- man/aggr.Rd | 430 +++++++++++++------------- man/alphablend.Rd | 62 +-- man/barMiss.Rd | 268 ++++++++-------- man/bgmap.Rd | 82 ++--- man/chorizonDL.Rd | 184 +++++------ man/colSequence.Rd | 150 ++++----- man/colormapMiss.Rd | 318 +++++++++---------- man/countInf.Rd | 58 +-- man/growdotMiss.Rd | 272 ++++++++-------- man/histMiss.Rd | 278 ++++++++--------- man/hotdeck.Rd | 128 +++---- man/initialise.Rd | 84 ++--- man/irmi.Rd | 238 +++++++------- man/kNN.Rd | 183 +++++------ man/kola.background.Rd | 46 +- man/mapMiss.Rd | 174 +++++----- man/marginmatrix.Rd | 152 ++++----- man/marginplot.Rd | 260 ++++++++-------- man/matrixplot.Rd | 244 +++++++-------- man/mosaicMiss.Rd | 184 +++++------ man/pairsVIM.Rd | 184 +++++------ man/parcoordMiss.Rd | 294 +++++++++--------- man/pbox.Rd | 250 +++++++-------- man/prepare.Rd | 152 ++++----- man/print.summary.aggr.Rd | 58 +-- man/regressionImp.Rd | 104 +++--- man/rugNA.Rd | 130 ++++---- man/scattJitt.Rd | 206 ++++++------ man/scattMiss.Rd | 234 +++++++------- man/scattmatrixMiss.Rd | 242 +++++++------- man/sleep.Rd | 58 +-- man/spineMiss.Rd | 294 +++++++++--------- man/tao.Rd | 60 +-- man/testdata.Rd | 60 +-- man/vmGUIenvir.Rd | 102 +++--- src/gowerD.cpp | 191 ++++++++--- tests |only 53 files changed, 4039 insertions(+), 3856 deletions(-)
Title: Simultaneous Signal Analysis
Description: Procedures for analyzing simultaneous signals, e.g., features that are simultaneously significant in two different studies. Includes methods for detecting simultaneous signals, for identifying them under false discovery rate control, and for leveraging them to improve prediction.
Author: Dave Zhao [aut, cre]
Maintainer: Dave Zhao <sdzhao@illinois.edu>
Diff between ssa versions 1.1.1 dated 2016-06-20 and 1.2.0 dated 2016-06-29
DESCRIPTION | 10 +++++----- MD5 | 28 +++++++++++++++++++++++++--- NAMESPACE | 19 +++++++++++++++++++ R/ldd.R | 2 +- R/link_fxns.R |only R/neb.R |only R/nebula.R |only R/npmle.R |only R/prs.R |only man/bi.npmle.Rd |only man/expit.Rd |only man/logit.Rd |only man/neb.predict.Rd |only man/neb.train.Rd |only man/nebula.bin.predict.Rd |only man/nebula.bin.train.Rd |only man/nebula.chisq.bin.predict.Rd |only man/nebula.chisq.bin.train.Rd |only man/nebula.chisq.predict.Rd |only man/nebula.chisq.train.Rd |only man/nebula.predict.Rd |only man/nebula.train.Rd |only man/prs.predict.Rd |only man/prs.train.Rd |only man/tri.npmle.Rd |only man/uni.npmle.Rd |only 26 files changed, 50 insertions(+), 9 deletions(-)
Title: Bayesian Geostatistical Modeling with RAMPS
Description: Bayesian geostatistical modeling of Gaussian processes using a reparameterized and marginalized posterior sampling (RAMPS) algorithm designed to lower autocorrelation in MCMC samples. Package performance is tuned for large spatial datasets.
Author: Brian J Smith [aut, cre],
Jun Yan [aut],
Mary Kathryn Cowles [aut]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between ramps versions 0.6-13 dated 2015-02-16 and 0.6-14 dated 2016-06-29
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NAMESPACE | 8 +++++++- data/NURE.rda |binary data/simJSS.rda |binary 5 files changed, 18 insertions(+), 11 deletions(-)
Title: COmbat CO-Normalization Using conTrols (COCONUT)
Description: Allows for pooled analysis of microarray data by batch-correcting control samples, and then applying the derived correction parameters to non-control samples to obtain bias-free, inter-dataset corrected data.
Author: Timothy E Sweeney, MD, PhD [aut,cre]
Maintainer: Timothy E Sweeney <tes17@alumni.stanford.edu>
Diff between COCONUT versions 1.0 dated 2016-06-14 and 1.0.1 dated 2016-06-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/COCONUT.R | 7 +++++-- build/partial.rdb |binary 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Visual Exploration of Protein Alignments Resulting from Multiple
Substitution Matrices
Description: Substitution matrices are important parameters in protein alignment algorithms. These matrices represent the likelihood that an amino acid will be substituted for another during mutation. This tool allows users to apply predefined and custom matrices and then explore the resulting alignments with interactive visualizations. SubVis requires the availability of a web browser.
Author: Scott Barlowe <sabarlowe@email.wcu.edu>
Maintainer: Scott Barlowe <sabarlowe@email.wcu.edu>
Diff between SubVis versions 1.0.0 dated 2016-06-16 and 1.1.0 dated 2016-06-29
DESCRIPTION | 12 ++++---- MD5 | 16 +++++----- inst/SubVisApp/js/SubVisDraw.js | 51 +++++++++++++++++++---------------- inst/SubVisApp/js/SubVisGetDecide.js | 40 ++++++++++++++++++++++----- inst/SubVisApp/js/SubVisGlobals.js | 3 +- inst/SubVisApp/ui.R | 4 +- inst/doc/SubVis.Rmd | 23 ++++++++------- inst/doc/SubVis.html | 29 ++++++++++--------- vignettes/SubVis.Rmd | 23 ++++++++------- 9 files changed, 119 insertions(+), 82 deletions(-)
Title: Import Articles from 'LexisNexis' Using the 'tm' Text Mining
Framework
Description: Provides a 'tm' Source to create corpora from
articles exported from the 'LexisNexis' content provider as
HTML files. It is able to read both text content and meta-data
information (including source, date, title, author and pages).
Note that the file format is highly unstable: there is no warranty
that this package will work for your corpus, and you may have
to adjust the code to adapt it to your particular format.
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between tm.plugin.lexisnexis versions 1.2 dated 2015-03-07 and 1.3 dated 2016-06-29
DESCRIPTION | 19 +++++++------ MD5 | 10 +++---- NAMESPACE | 2 - NEWS | 3 ++ R/LexisNexisSource.R | 12 +++++++- R/readLexisNexisHTML.R | 69 +++++++++++++++++++++++++------------------------ 6 files changed, 66 insertions(+), 49 deletions(-)
More information about tm.plugin.lexisnexis at CRAN
Permanent link
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.9.3 dated 2016-03-29 and 0.9.4 dated 2016-06-29
DESCRIPTION | 12 MD5 | 141 +++--- NAMESPACE | 1 NEWS.md |only R/check_wkt.r | 2 R/dataset_search.r | 58 +- R/dataset_suggest.r | 50 +- R/datasets.r | 52 +- R/elevation.r | 6 R/gbif_citation.R | 2 R/gbif_names.R | 2 R/gbif_photos.r | 2 R/gbifmap.r | 8 R/installations.r | 39 + R/name_backbone.r | 4 R/name_lookup.r | 10 R/name_suggest.r | 6 R/name_usage.r | 10 R/networks.r | 34 - R/nodes.r | 12 R/occ_data.R | 12 R/occ_download.R | 39 + R/occ_download_cancel.R | 4 R/occ_download_get.r | 4 R/occ_download_import.R | 2 R/occ_download_list.R | 4 R/occ_download_meta.R | 4 R/occ_issues.r | 8 R/occ_search.r | 39 + R/organizations.r | 60 -- R/rgbif-package.r | 3 R/tbl_df_utils.R | 2 R/zzz.r | 54 ++ README.md | 232 ++++++----- build/vignette.rds |binary inst/assets/img/unnamed-chunk-8-1.png |binary inst/doc/issues_vignette.Rmd | 318 +++++++-------- inst/doc/issues_vignette.html | 318 +++++++-------- inst/doc/rgbif_vignette.html | 674 +++++++++++++-------------------- inst/doc/taxonomic_names.Rmd |only inst/doc/taxonomic_names.html |only inst/vign/figure/gbifmap1-1.png |binary inst/vign/issues_vignette.md | 318 +++++++-------- inst/vign/rgbif_vignette.Rmd | 2 inst/vign/rgbif_vignette.md | 672 +++++++++++++------------------- inst/vign/taxonomic_names.Rmd |only inst/vign/taxonomic_names.md |only man/dataset_search.Rd | 14 man/dataset_suggest.Rd | 16 man/datasets.Rd | 16 man/elevation.Rd | 4 man/gbifmap.Rd | 14 man/installations.Rd | 13 man/name_lookup.Rd | 2 man/networks.Rd | 14 man/nodes.Rd | 10 man/occ_data.Rd | 44 +- man/occ_search.Rd | 4 man/organizations.Rd | 13 man/rgbif-package.Rd | 2 tests/testthat/test-dataset_search.r | 40 + tests/testthat/test-dataset_suggest.r | 18 tests/testthat/test-download_parsing.R |only tests/testthat/test-name_lookup.r | 5 tests/testthat/test-name_suggest.r | 4 tests/testthat/test-name_usage.r | 8 tests/testthat/test-nodes.r | 2 tests/testthat/test-occ_count.r | 4 tests/testthat/test-occ_data.R | 18 tests/testthat/test-occ_issues.R | 14 tests/testthat/test-occ_search.r | 26 - tests/testthat/test-wkt_large.R | 6 vignettes/issues_vignette.Rmd | 318 +++++++-------- vignettes/rgbif_vignette.Rmd | 672 +++++++++++++------------------- vignettes/taxonomic_names.Rmd |only 75 files changed, 2112 insertions(+), 2409 deletions(-)
Title: Multiplicative Competitive Interaction (MCI) Model
Description: The Multiplicative Competitive Interaction (MCI) Model by Nakanishi & Cooper (1974) <DOI:10.2307/3151146> is an econometric model for analyzing market shares and/or market areas. The functions in this package include fitting the MCI model, MCI shares simulations, the log-centering transformation of MCI datasets, creation of interaction matrices and tools for data preparation.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Diff between MCI versions 1.1.0 dated 2016-06-16 and 1.1.1 dated 2016-06-29
MCI-1.1.0/MCI/R/var.check.R |only MCI-1.1.0/MCI/R/var.zetas.R |only MCI-1.1.0/MCI/man/var.check.Rd |only MCI-1.1.0/MCI/man/var.zetas.Rd |only MCI-1.1.1/MCI/DESCRIPTION | 8 - MCI-1.1.1/MCI/MD5 | 68 +++++++------- MCI-1.1.1/MCI/NAMESPACE | 2 MCI-1.1.1/MCI/R/checkdf.R |only MCI-1.1.1/MCI/R/checkvar.R |only MCI-1.1.1/MCI/R/geom.R | 2 MCI-1.1.1/MCI/R/ijmatrix.create.R | 161 +++++++++++++++++++++++++++++++---- MCI-1.1.1/MCI/R/ijmatrix.shares.R | 34 ++++++- MCI-1.1.1/MCI/R/mci.fit.R | 7 + MCI-1.1.1/MCI/R/mci.shares.R | 39 +++++++- MCI-1.1.1/MCI/R/mci.transmat.R | 33 ++++++- MCI-1.1.1/MCI/R/mci.transvar.R | 41 +++++++- MCI-1.1.1/MCI/R/shares.total.R | 26 ++++- MCI-1.1.1/MCI/R/var.asdummy.R | 11 ++ MCI-1.1.1/MCI/R/var.correct.R | 28 +++++- MCI-1.1.1/MCI/data/Freiburg1.rda |binary MCI-1.1.1/MCI/data/Freiburg2.rda |binary MCI-1.1.1/MCI/data/ce.rda |binary MCI-1.1.1/MCI/data/grocery1.rda |binary MCI-1.1.1/MCI/data/grocery2.rda |binary MCI-1.1.1/MCI/man/Freiburg1.Rd | 11 +- MCI-1.1.1/MCI/man/Freiburg2.Rd | 15 +-- MCI-1.1.1/MCI/man/MCI-package.Rd | 6 + MCI-1.1.1/MCI/man/ce.Rd | 6 - MCI-1.1.1/MCI/man/grocery1.Rd | 4 MCI-1.1.1/MCI/man/grocery2.Rd | 4 MCI-1.1.1/MCI/man/ijmatrix.create.Rd | 27 +++++ MCI-1.1.1/MCI/man/ijmatrix.shares.Rd | 18 ++- MCI-1.1.1/MCI/man/mci.fit.Rd | 10 +- MCI-1.1.1/MCI/man/mci.shares.Rd | 22 ++-- MCI-1.1.1/MCI/man/mci.transmat.Rd | 6 + MCI-1.1.1/MCI/man/mci.transvar.Rd | 10 +- MCI-1.1.1/MCI/man/shares.total.Rd | 12 +- MCI-1.1.1/MCI/man/var.correct.Rd | 28 +++--- 38 files changed, 487 insertions(+), 152 deletions(-)
Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++.
Author: Davide Altomare
Maintainer: Davide Altomare <davide.altomare@gmail.com>
Diff between ChannelAttribution versions 1.5 dated 2016-01-25 and 1.6 dated 2016-06-29
DESCRIPTION | 9 +- MD5 | 12 +-- R/ChannelAttribution.R | 8 +- man/ChannelAttribution-package.Rd | 5 - man/markov_model.Rd | 7 - src/ChannelAttribution.cpp | 143 +++++++++++++++----------------------- src/ChannelAttribution.h | 2 7 files changed, 80 insertions(+), 106 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Applied Statistical Time Series Analysis
Description: Contains data sets and scripts to accompany Time Series Analysis and Its Applications: With R Examples by Shumway and Stoffer, fourth edition.
Author: David Stoffer
Maintainer: David Stoffer <stoffer@pitt.edu>
Diff between astsa versions 1.3 dated 2014-10-27 and 1.4 dated 2016-06-29
astsa-1.3/astsa/data/ar1boot.rda |only astsa-1.3/astsa/man/ar1boot.Rd |only astsa-1.4/astsa/ChangeLog | 16 +++ astsa-1.4/astsa/DESCRIPTION | 12 +- astsa-1.4/astsa/MD5 | 164 +++++++++++++++++------------------ astsa-1.4/astsa/NAMESPACE | 9 + astsa-1.4/astsa/R/FDR.R | 4 astsa-1.4/astsa/R/LagReg.R | 28 +++-- astsa-1.4/astsa/R/SigExtract.R | 10 ++ astsa-1.4/astsa/R/acf2.R | 12 +- astsa-1.4/astsa/R/arma.spec.R | 22 ++-- astsa-1.4/astsa/R/lag1.plot.R | 18 ++- astsa-1.4/astsa/R/lag2.plot.R | 18 ++- astsa-1.4/astsa/R/mvspec.R | 11 ++ astsa-1.4/astsa/R/sarima.R | 20 +++- astsa-1.4/astsa/R/sarima.for.R | 13 ++ astsa-1.4/astsa/R/stoch.reg.R | 7 + astsa-1.4/astsa/data/EQcount.rda |only astsa-1.4/astsa/data/ar1miss.rda |binary astsa-1.4/astsa/data/sp500w.rda |only astsa-1.4/astsa/man/EM0.Rd | 4 astsa-1.4/astsa/man/EM1.Rd | 6 - astsa-1.4/astsa/man/EQ5.Rd | 3 astsa-1.4/astsa/man/EQcount.Rd |only astsa-1.4/astsa/man/EXP6.Rd | 1 astsa-1.4/astsa/man/FDR.Rd | 2 astsa-1.4/astsa/man/HCT.Rd | 3 astsa-1.4/astsa/man/Kfilter0.Rd | 4 astsa-1.4/astsa/man/Kfilter1.Rd | 6 - astsa-1.4/astsa/man/Kfilter2.Rd | 6 - astsa-1.4/astsa/man/Ksmooth0.Rd | 6 - astsa-1.4/astsa/man/Ksmooth1.Rd | 6 - astsa-1.4/astsa/man/Ksmooth2.Rd | 6 - astsa-1.4/astsa/man/LagReg.Rd | 10 +- astsa-1.4/astsa/man/PLT.Rd | 2 astsa-1.4/astsa/man/SVfilter.Rd | 4 astsa-1.4/astsa/man/SigExtract.Rd | 4 astsa-1.4/astsa/man/WBC.Rd | 3 astsa-1.4/astsa/man/acf2.Rd | 2 astsa-1.4/astsa/man/ar1miss.Rd | 10 -- astsa-1.4/astsa/man/arf.Rd | 3 astsa-1.4/astsa/man/arma.spec.Rd | 10 +- astsa-1.4/astsa/man/astsa-package.Rd | 8 - astsa-1.4/astsa/man/beamd.Rd | 4 astsa-1.4/astsa/man/birth.Rd | 3 astsa-1.4/astsa/man/blood.Rd | 5 - astsa-1.4/astsa/man/bnrf1ebv.Rd | 5 - astsa-1.4/astsa/man/bnrf1hvs.Rd | 5 - astsa-1.4/astsa/man/climhyd.Rd | 8 - astsa-1.4/astsa/man/cmort.Rd | 3 astsa-1.4/astsa/man/econ5.Rd | 2 astsa-1.4/astsa/man/eqexp.Rd | 3 astsa-1.4/astsa/man/flu.Rd | 2 astsa-1.4/astsa/man/fmri.Rd | 63 ------------- astsa-1.4/astsa/man/fmri1.Rd | 3 astsa-1.4/astsa/man/gas.Rd | 3 astsa-1.4/astsa/man/gnp.Rd | 3 astsa-1.4/astsa/man/gtemp.Rd | 2 astsa-1.4/astsa/man/gtemp2.Rd | 2 astsa-1.4/astsa/man/jj.Rd | 3 astsa-1.4/astsa/man/lag1.plot.Rd | 7 - astsa-1.4/astsa/man/lag2.plot.Rd | 7 - astsa-1.4/astsa/man/lap.Rd | 3 astsa-1.4/astsa/man/mvspec.Rd | 4 astsa-1.4/astsa/man/oil.Rd | 1 astsa-1.4/astsa/man/part.Rd | 1 astsa-1.4/astsa/man/prodn.Rd | 2 astsa-1.4/astsa/man/qinfl.Rd | 3 astsa-1.4/astsa/man/qintr.Rd | 3 astsa-1.4/astsa/man/rec.Rd | 2 astsa-1.4/astsa/man/sales.Rd | 1 astsa-1.4/astsa/man/salt.Rd | 2 astsa-1.4/astsa/man/saltemp.Rd | 2 astsa-1.4/astsa/man/sarima.Rd | 4 astsa-1.4/astsa/man/sarima.for.Rd | 4 astsa-1.4/astsa/man/so2.Rd | 1 astsa-1.4/astsa/man/soi.Rd | 3 astsa-1.4/astsa/man/soiltemp.Rd | 3 astsa-1.4/astsa/man/sp500w.Rd |only astsa-1.4/astsa/man/speech.Rd | 3 astsa-1.4/astsa/man/star.Rd | 3 astsa-1.4/astsa/man/stoch.reg.Rd | 4 astsa-1.4/astsa/man/sunspotz.Rd | 3 astsa-1.4/astsa/man/tempr.Rd | 1 astsa-1.4/astsa/man/unemp.Rd | 2 astsa-1.4/astsa/man/varve.Rd | 3 86 files changed, 336 insertions(+), 328 deletions(-)
Title: Power Calculations for SNP Studies with Censored Outcomes
Description: Conduct asymptotic and empirical power and sample size calculations for Single-Nucleotide Polymorphism (SNP) association studies with right censored time to event outcomes.
Author: Kouros Owzar, Zhiguo Li, Nancy Cox, Sin-Ho Jung and Chanhee Yi
Maintainer: Alexander Sibley <alexander.sibley@dm.duke.edu>
Diff between survSNP versions 0.23.2 dated 2015-01-18 and 0.24 dated 2016-06-29
survSNP-0.23.2/survSNP/R/zzz.R |only survSNP-0.23.2/survSNP/inst/doc/survSNP-knitr.R |only survSNP-0.23.2/survSNP/inst/doc/survSNP-knitr.Rnw |only survSNP-0.23.2/survSNP/inst/doc/survSNP-knitr.pdf |only survSNP-0.23.2/survSNP/vignettes/survSNP-knitr.Rnw |only survSNP-0.24/survSNP/DESCRIPTION | 12 +++--- survSNP-0.24/survSNP/MD5 | 40 ++++++++++----------- survSNP-0.24/survSNP/NAMESPACE | 3 + survSNP-0.24/survSNP/NEWS |only survSNP-0.24/survSNP/R/sim.snp.expsurv.power.R | 20 ++-------- survSNP-0.24/survSNP/R/sim.snp.expsurv.sctest.R | 10 +---- survSNP-0.24/survSNP/R/survSNP.power.table.R | 2 - survSNP-0.24/survSNP/build/vignette.rds |binary survSNP-0.24/survSNP/inst/doc/survSNP.R |only survSNP-0.24/survSNP/inst/doc/survSNP.Rnw |only survSNP-0.24/survSNP/inst/doc/survSNP.pdf |only survSNP-0.24/survSNP/man/asypow.Rd | 2 - survSNP-0.24/survSNP/man/censbnd.Rd | 2 - survSNP-0.24/survSNP/man/hwe.Rd | 2 - survSNP-0.24/survSNP/man/sim.snp.expsurv.power.Rd | 2 - survSNP-0.24/survSNP/man/sim.snp.expsurv.sctest.Rd | 2 - survSNP-0.24/survSNP/man/surv.exp.gt.model.Rd | 4 +- survSNP-0.24/survSNP/man/survSNP-package.Rd | 13 +++--- survSNP-0.24/survSNP/man/survSNP.power.table.Rd | 10 +---- survSNP-0.24/survSNP/src/Makevars.win | 26 ++++++------- survSNP-0.24/survSNP/vignettes/survSNP.Rnw |only 26 files changed, 66 insertions(+), 84 deletions(-)
Title: Bayesian Spatial Survival Analysis with Parametric Proportional
Hazards Models
Description: Bayesian inference for parametric proportional hazards spatial
survival models; flexible spatial survival models.
Author: Benjamin M. Taylor and Barry S. Rowlingson
Additional contributions
Ziyu Zheng
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between spatsurv versions 0.9-11 dated 2015-10-21 and 0.9-12 dated 2016-06-29
DESCRIPTION | 16 - MD5 | 363 +++++++++++++------------- NAMESPACE | 25 + R/BsplineHaz.R | 14 - R/PsplineHaz.R |only R/RWprior.R |only R/baseHazST.R |only R/baseHazST_prior.R |only R/calibratemcmc.R | 112 +++++--- R/covarianceFunctions.R | 23 + R/exponential.R | 42 +-- R/gompertz.R | 42 +-- R/log_posteriors_and_derivatives.R | 102 ++++++- R/log_posteriors_and_derivatives_SPDE.R | 102 ++++++- R/log_posteriors_and_derivatives_gridded.R | 106 ++++++- R/log_posteriors_and_derivatives_polygonal.R | 104 ++++++- R/makeham.R | 42 +-- R/nonspatial_log_likelihood_and_derivatives.R | 37 ++ R/optifix.R |only R/partial_likelihood.R |only R/plottingfunctions.R | 19 - R/postprocessing.R | 143 +++++++++- R/spatgrid.R | 22 + R/spatial_imputation.R |only R/spatsurv.R | 9 R/spatsurvMisc.R | 49 +++ R/survsim.R | 2 R/survspat.R | 240 +++++++++++++++-- R/tpow.R | 42 +-- R/weibull.R | 42 +-- data/fs.rda |binary data/fstimes.rda |binary man/B.Rd | 2 man/Bspline.construct.Rd | 2 man/BsplineHaz.Rd | 32 +- man/CSplot.Rd | 2 man/Et_PP.Rd | 2 man/EvalCov.Rd | 2 man/ExponentialCovFct.Rd | 2 man/FFTgrid.Rd | 6 man/GammaFromY_SPDE.Rd | 2 man/GammafromY.Rd | 2 man/Independent.Rd |only man/MCE.Rd | 6 man/NonSpatialLogLikelihood_or_gradient.Rd | 2 man/PsplineHaz.Rd |only man/QuadApprox.Rd | 4 man/SPDE.Rd | 2 man/SPDEprec.Rd | 2 man/SpikedExponentialCovFct.Rd | 2 man/Summarise.Rd | 2 man/YFromGamma_SPDE.Rd | 2 man/YfromGamma.Rd | 2 man/allocate.Rd | 2 man/alpha.Rd | 2 man/baseHazST.Rd |only man/basehazard.Rd | 2 man/basehazard.basehazardspec.Rd | 2 man/baselinehazard.Rd | 4 man/betapriorGauss.Rd | 2 man/boxplotRisk.Rd |only man/checkSurvivalData.Rd | 2 man/circulant.Rd | 2 man/circulant.matrix.Rd | 4 man/circulant.numeric.Rd | 2 man/circulantij.Rd | 2 man/covmodel.Rd | 4 man/cumbasehazard.Rd | 2 man/cumbasehazard.basehazardspec.Rd | 2 man/cumulativeBspline.construct.Rd | 2 man/density_PP.Rd | 2 man/densityquantile.Rd | 2 man/densityquantile.basehazardspec.Rd | 2 man/densityquantile_PP.Rd | 2 man/derivindepGaussianprior.Rd | 2 man/derivindepGaussianpriorST.Rd |only man/derivpsplineprior.Rd |only man/distinfo.Rd | 2 man/distinfo.basehazardspec.Rd | 2 man/estimateY.Rd | 2 man/etapriorGauss.Rd | 2 man/exponentialHaz.Rd | 32 +- man/fixedpars.Rd | 4 man/fixmatrix.Rd | 2 man/frailtylag1.Rd | 4 man/gamma2risk.Rd |only man/gencens.Rd | 4 man/getBackground.Rd | 6 man/getBbasis.Rd | 2 man/getGrid.Rd | 2 man/getOptCellwidth.Rd | 8 man/getbb.Rd | 2 man/getcov.Rd | 2 man/getgrd.Rd | 2 man/getleneta.Rd | 2 man/getparranges.Rd | 2 man/getsurvdata.Rd | 2 man/gompertzHaz.Rd | 32 +- man/gradbasehazard.Rd | 2 man/gradbasehazard.basehazardspec.Rd | 2 man/gradcumbasehazard.Rd | 2 man/gradcumbasehazard.basehazardspec.Rd | 2 man/grid2spdf.Rd | 2 man/grid2spix.Rd | 2 man/grid2spts.Rd | 2 man/gridY.Rd | 2 man/gridY_polygonal.Rd | 2 man/guess_t.Rd | 2 man/hasNext.Rd | 2 man/hasNext.iter.Rd | 2 man/hazard_PP.Rd | 2 man/hazardexceedance.Rd | 4 man/hazardpars.Rd | 4 man/hessbasehazard.Rd | 2 man/hessbasehazard.basehazardspec.Rd | 2 man/hesscumbasehazard.Rd | 2 man/hesscumbasehazard.basehazardspec.Rd | 2 man/imputationModel.Rd |only man/indepGaussianprior.Rd | 2 man/indepGaussianpriorST.Rd |only man/inference.control.Rd | 22 + man/invtransformweibull.Rd | 4 man/is.burnin.Rd | 2 man/is.retain.Rd | 2 man/iteration.Rd | 2 man/logPosterior.Rd | 2 man/logPosterior_SPDE.Rd | 2 man/logPosterior_gridded.Rd | 2 man/logPosterior_polygonal.Rd | 2 man/loop.mcmc.Rd | 2 man/makehamHaz.Rd | 32 +- man/maxlikparamPHsurv.Rd | 2 man/mcmcLoop.Rd | 2 man/mcmcPriors.Rd | 12 man/mcmcProgressNone.Rd | 2 man/mcmcProgressPrint.Rd | 2 man/mcmcProgressTextBar.Rd | 2 man/mcmcpars.Rd | 2 man/midpts.Rd | 2 man/neighLocs.Rd | 2 man/neighOrder.Rd | 2 man/nextStep.Rd | 2 man/omegapriorGauss.Rd | 2 man/omegapriorGaussST.Rd |only man/optifix.Rd |only man/plotsurv.Rd | 2 man/polyadd.Rd | 4 man/polymult.Rd | 4 man/posteriorcov.Rd | 8 man/predict.mcmcspatsurv.Rd | 6 man/print.mcmc.Rd | 2 man/print.mcmcspatsurv.Rd | 4 man/print.mlspatsurv.Rd | 4 man/print.textSummary.Rd | 2 man/priorposterior.Rd | 4 man/proposalVariance.Rd | 2 man/proposalVariance_SPDE.Rd | 2 man/proposalVariance_gridded.Rd | 2 man/proposalVariance_polygonal.Rd | 2 man/psplineRWprior.Rd |only man/psplineprior.Rd |only man/quantile.mcmcspatsurv.Rd | 4 man/quantile.mlspatsurv.Rd | 4 man/randompars.Rd | 4 man/reconstruct.bs.Rd | 26 - man/reconstruct.bs.coxph.Rd |only man/reconstruct.bs.mcmcspatsurv.Rd |only man/resetLoop.Rd | 2 man/residuals.mcmcspatsurv.Rd | 2 man/setTxtProgressBar2.Rd | 2 man/setupHazard.Rd | 4 man/setupPrecMatStruct.Rd | 2 man/showGrid.Rd | 6 man/simsurv.Rd | 6 man/spatialpars.Rd | 4 man/spatsurv-package.Rd | 7 man/spatsurvVignette.Rd | 2 man/spplot1.Rd | 7 man/spplot_compare.Rd | 4 man/summary.mcmc.Rd | 2 man/summary.mcmcspatsurv.Rd | 4 man/surv3d.Rd | 2 man/survival_PP.Rd | 2 man/survspat.Rd | 10 man/survspatNS.Rd | 4 man/textSummary.Rd | 2 man/timevaryingPL.Rd |only man/tpowHaz.Rd | 32 +- man/transformweibull.Rd | 4 man/txtProgressBar2.Rd | 2 man/urlTemplate.Rd | 16 - man/vcov.mcmcspatsurv.Rd | 4 man/vcov.mlspatsurv.Rd | 4 man/weibullHaz.Rd | 32 +- 194 files changed, 1583 insertions(+), 761 deletions(-)
Title: Subgroup Identification Based on Differential Effect Search
Description: Provides function to apply "Subgroup Identification based on Differential Effect Search" (SIDES) method proposed by Lipkovich et al. (2011) <doi:10.1002/sim.4289>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between SIDES versions 1.0 dated 2016-06-02 and 1.1 dated 2016-06-29
DESCRIPTION | 12 +-- MD5 | 14 ++-- NAMESPACE | 4 - R/RESAMPLING_METHOD.R | 1 R/SIDES_MAIN.R | 159 ++++++++++++++++++++++++++++++++++++++++++------ man/SIDES-package.Rd | 4 - man/SIDES.Rd | 6 - man/simulation_SIDES.Rd | 11 +-- 8 files changed, 165 insertions(+), 46 deletions(-)
Title: Multivariate Nonparametric Methods. An Approach Based on Spatial
Signs and Ranks
Description: Multivariate tests, estimates and methods based on the identity score, spatial sign score and spatial rank score are provided. The methods include one and c-sample problems, shape estimation and testing, linear regression and principal components.
Author: Klaus Nordhausen, Jyrki Mottonen, Hannu Oja
Maintainer: Klaus Nordhausen <klaus.nordhausen@utu.fi>
Diff between MNM versions 1.0-1 dated 2015-01-09 and 1.0-2 dated 2016-06-29
DESCRIPTION | 10 +++++----- MD5 | 29 +++++++++++++++-------------- NAMESPACE | 1 + R/MNMinternals.R |only R/csampleinternal.R | 10 +++++----- R/locEst.R | 8 ++++---- R/locTestInternal.R | 7 ++++--- R/mv.2way.estInternal.R | 2 +- R/mv.l1lm.Internal.R | 18 +++++++++--------- R/mv2sampleEstInternal.R | 8 ++++---- R/mvshapetest_internal.R | 36 ++++++++++++++++++++++++++---------- R/rmvpowerexp.R | 2 +- R/spatial.sign2.R | 2 +- data/beans.rda |binary inst/ChangeLog | 5 +++++ man/MNM-package.Rd | 4 ++-- 16 files changed, 83 insertions(+), 59 deletions(-)
Title: Simulation of Ecological Models
Description: Computer simulations of classical ecological models as a
learning resource.
Author: Alexandre Adalardo de Oliveira and Paulo Inacio Prado
<ecovirtualpackage@gmail.com>
Maintainer: Alexandre Adalardo de Oliveira <ecovirtualpackage@gmail.com>
Diff between EcoVirtual versions 0.1 dated 2014-08-16 and 1.0 dated 2016-06-29
EcoVirtual-0.1/EcoVirtual/man/metapopulation.Rd |only EcoVirtual-1.0/EcoVirtual/DESCRIPTION | 15 EcoVirtual-1.0/EcoVirtual/MD5 | 46 +- EcoVirtual-1.0/EcoVirtual/NAMESPACE | 43 +- EcoVirtual-1.0/EcoVirtual/R/bioGeo.R | 463 ++++++++++++++++++------ EcoVirtual-1.0/EcoVirtual/R/dynPop.R | 245 ++++++++++-- EcoVirtual-1.0/EcoVirtual/R/intEcoVirtual.R | 211 ++++++++-- EcoVirtual-1.0/EcoVirtual/R/metaPop.R | 257 +++++++++---- EcoVirtual-1.0/EcoVirtual/R/multSp.R | 147 +++++++ EcoVirtual-1.0/EcoVirtual/R/twoSp.R | 210 +++++++--- EcoVirtual-1.0/EcoVirtual/man/anima.Rd | 61 +-- EcoVirtual-1.0/EcoVirtual/man/animaColExt.Rd | 83 ++-- EcoVirtual-1.0/EcoVirtual/man/archip.Rd | 122 ++---- EcoVirtual-1.0/EcoVirtual/man/bioGeoIsl.Rd | 120 ++---- EcoVirtual-1.0/EcoVirtual/man/comCompete.Rd | 97 ++--- EcoVirtual-1.0/EcoVirtual/man/compLV.Rd | 109 ++--- EcoVirtual-1.0/EcoVirtual/man/dynPop.Rd | 220 ++++++----- EcoVirtual-1.0/EcoVirtual/man/extGame.Rd | 77 +-- EcoVirtual-1.0/EcoVirtual/man/metaComp.Rd | 114 ++--- EcoVirtual-1.0/EcoVirtual/man/metaPop.Rd |only EcoVirtual-1.0/EcoVirtual/man/randWalk.Rd | 86 ++-- EcoVirtual-1.0/EcoVirtual/man/regNicho.Rd | 135 +++--- EcoVirtual-1.0/EcoVirtual/man/rich.Rd | 47 +- EcoVirtual-1.0/EcoVirtual/man/simHub.Rd | 122 +++--- EcoVirtual-1.0/EcoVirtual/man/sucMatrix.Rd | 69 +-- 25 files changed, 1929 insertions(+), 1170 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized (non-)linear mixed models using Stan for full
Bayesian inference.
Author: Paul-Christian Buerkner [aut, cre]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 0.9.1 dated 2016-05-17 and 0.10.0 dated 2016-06-29
brms-0.10.0/brms/DESCRIPTION | 21 brms-0.10.0/brms/MD5 | 165 ++-- brms-0.10.0/brms/NAMESPACE | 6 brms-0.10.0/brms/R/brm.R | 115 +-- brms-0.10.0/brms/R/brmsfit-helpers.R | 51 - brms-0.10.0/brms/R/brmsfit-methods.R | 381 +++++++--- brms-0.10.0/brms/R/correlations.R | 51 + brms-0.10.0/brms/R/data-helpers.R | 151 ++- brms-0.10.0/brms/R/extract_draws.R | 91 +- brms-0.10.0/brms/R/families.R | 67 + brms-0.10.0/brms/R/fitted.R | 159 ++-- brms-0.10.0/brms/R/generics.R | 28 brms-0.10.0/brms/R/linear_predictor.R | 19 brms-0.10.0/brms/R/loglik.R | 2 brms-0.10.0/brms/R/lsp.R |only brms-0.10.0/brms/R/make_stancode.R | 9 brms-0.10.0/brms/R/make_standata.R | 59 - brms-0.10.0/brms/R/misc-methods.R | 13 brms-0.10.0/brms/R/misc.R | 15 brms-0.10.0/brms/R/predict.R | 12 brms-0.10.0/brms/R/priors.R | 154 ++-- brms-0.10.0/brms/R/rename.R | 72 + brms-0.10.0/brms/R/stan-helpers.R | 160 ++-- brms-0.10.0/brms/R/stan-predictor.R | 190 +++- brms-0.10.0/brms/R/validate.R | 216 ++++- brms-0.10.0/brms/R/zzz.R | 11 brms-0.10.0/brms/README.md | 17 brms-0.10.0/brms/build/vignette.rds |binary brms-0.10.0/brms/inst/NEWS.Rd | 44 + brms-0.10.0/brms/inst/chunks/fun_as_matrix.stan | 2 brms-0.10.0/brms/inst/chunks/fun_cauchit.stan | 21 brms-0.10.0/brms/inst/chunks/fun_cloglog.stan |only brms-0.10.0/brms/inst/chunks/fun_cov_matrix_ar1.stan | 8 brms-0.10.0/brms/inst/chunks/fun_cov_matrix_arma1.stan | 10 brms-0.10.0/brms/inst/chunks/fun_cov_matrix_ma1.stan | 10 brms-0.10.0/brms/inst/chunks/fun_hurdle_gamma.stan | 8 brms-0.10.0/brms/inst/chunks/fun_hurdle_negbinomial.stan | 10 brms-0.10.0/brms/inst/chunks/fun_hurdle_poisson.stan | 8 brms-0.10.0/brms/inst/chunks/fun_inv_gaussian_ccdf.stan | 4 brms-0.10.0/brms/inst/chunks/fun_inv_gaussian_cdf.stan | 4 brms-0.10.0/brms/inst/chunks/fun_inv_gaussian_pw.stan | 2 brms-0.10.0/brms/inst/chunks/fun_inv_gaussian_vector.stan | 2 brms-0.10.0/brms/inst/chunks/fun_kronecker.stan | 2 brms-0.10.0/brms/inst/chunks/fun_monotonic.stan |only brms-0.10.0/brms/inst/chunks/fun_normal_cov.stan | 12 brms-0.10.0/brms/inst/chunks/fun_student_t_cov.stan | 10 brms-0.10.0/brms/inst/chunks/fun_zero_inflated_beta.stan | 16 brms-0.10.0/brms/inst/chunks/fun_zero_inflated_binomial.stan | 14 brms-0.10.0/brms/inst/chunks/fun_zero_inflated_negbinomial.stan | 14 brms-0.10.0/brms/inst/chunks/fun_zero_inflated_poisson.stan | 12 brms-0.10.0/brms/inst/chunks/tdata_calc_sparse_X.stan | 6 brms-0.10.0/brms/inst/doc/brms.ltx | 10 brms-0.10.0/brms/inst/doc/brms.pdf |binary brms-0.10.0/brms/man/as.mcmc.brmsfit.Rd | 2 brms-0.10.0/brms/man/brm.Rd | 86 +- brms-0.10.0/brms/man/brmsfamily.Rd | 4 brms-0.10.0/brms/man/cor_bsts.Rd |only brms-0.10.0/brms/man/fitted.brmsfit.Rd | 22 brms-0.10.0/brms/man/get_prior.Rd | 2 brms-0.10.0/brms/man/make_stancode.Rd | 12 brms-0.10.0/brms/man/make_standata.Rd | 8 brms-0.10.0/brms/man/marginal_effects.Rd | 7 brms-0.10.0/brms/man/posterior_samples.Rd | 18 brms-0.10.0/brms/man/predict.brmsfit.Rd | 24 brms-0.10.0/brms/man/residuals.brmsfit.Rd | 22 brms-0.10.0/brms/man/set_prior.Rd | 26 brms-0.10.0/brms/man/update.brmsfit.Rd | 7 brms-0.10.0/brms/tests/testthat/tests.brm.R | 2 brms-0.10.0/brms/tests/testthat/tests.brmsfit-helpers.R | 5 brms-0.10.0/brms/tests/testthat/tests.brmsfit-methods.R | 96 +- brms-0.10.0/brms/tests/testthat/tests.data-helpers.R | 30 brms-0.10.0/brms/tests/testthat/tests.fitted.R | 35 brms-0.10.0/brms/tests/testthat/tests.loglik.R | 3 brms-0.10.0/brms/tests/testthat/tests.make_stancode.R | 98 +- brms-0.10.0/brms/tests/testthat/tests.make_standata.R | 36 brms-0.10.0/brms/tests/testthat/tests.misc.R | 7 brms-0.10.0/brms/tests/testthat/tests.nonlinear_predictor.R | 4 brms-0.10.0/brms/tests/testthat/tests.plots.R | 2 brms-0.10.0/brms/tests/testthat/tests.predict.R | 3 brms-0.10.0/brms/tests/testthat/tests.priors.R | 26 brms-0.10.0/brms/tests/testthat/tests.stan-helpers.R | 55 - brms-0.10.0/brms/tests/testthat/tests.stan_functions.R | 44 - brms-0.10.0/brms/tests/testthat/tests.validate.R | 39 - brms-0.10.0/brms/vignettes/brms.ltx | 10 brms-0.10.0/brms/vignettes/kidney_marginal_effects.pdf |binary brms-0.9.1/brms/inst/chunks/fun_monotonous.stan |only 86 files changed, 2160 insertions(+), 1039 deletions(-)
Title: A Collection of Handy, Useful Functions
Description: A set of little functions that have been found useful to do little
odds and ends such as plotting the results of K-means clustering, substituting
special text characters, viewing parts of a data.frame, constructing formulas
from text and building design and response matrices.
Author: Jared P. Lander
Maintainer: Jared P. Lander <packages@jaredlander.com>
Diff between useful versions 1.2.0 dated 2016-01-10 and 1.2.1 dated 2016-06-29
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++++----- NAMESPACE | 1 + NEWS.md | 6 +++++- R/knitting.r |only R/unique.r |only README.md | 2 +- man/uniqueBidirection.Rd |only tests/testthat/test-simple-impute.r | 8 ++++---- tests/testthat/test-unique.R |only 10 files changed, 24 insertions(+), 15 deletions(-)
Title: Unification of Clustering Results from Multiple Datasets using
External Specifications
Description: Consensus clustering by the unification of clustering results from multiple datasets using external specifications.
Author: Basel Abu-Jamous
Maintainer: Basel Abu-Jamous <baselabujamous@gmail.com>
Diff between UNCLES versions 1.0 dated 2016-05-04 and 2.0 dated 2016-06-29
DESCRIPTION | 10 MD5 | 65 ++++-- NAMESPACE | 6 R/HC.R |only R/KA.R |only R/SOMs.R |only R/binarise.R | 28 ++ R/closestToSquareFactors.R |only R/clustDist.R |only R/clustVec2partMat.R |only R/clusterDataset.R | 49 ++++ R/factors.R |only R/fixnans.R | 58 +++++ R/fuzzystretch.R |only R/generateCoPaM.R | 102 +++++++++ R/isValidBPM.R |only R/isempty.R |only R/isnullorempty.R |only R/kmeansKA.R |only R/mnplots.R | 296 ++++++++++++++++++++++++++++ R/mseclusters.R | 93 ++++++++ R/normaliseMatrix.R | 78 +++++++ R/partMat2clustVec.R |only R/permutations.R |only R/relabelClusts.R | 140 +++++++++++++ R/uncles.R | 367 ++++++++++++++++++++++++++++++++++- build/partial.rdb |binary inst |only man/HC.Rd |only man/KA.Rd |only man/SOMs.Rd |only man/binarise.Rd | 8 man/closestToSquareFactors.Rd |only man/clustDist.Rd |only man/clustVec2partMat.Rd |only man/clusterDataset.Rd | 2 man/factors.Rd |only man/fuzzystretch.Rd |only man/isValidBPM.Rd |only man/isempty.Rd |only man/isnullorempty.Rd |only man/kmeansKA.Rd |only man/mnplots.Rd | 210 +++++++++++++++++--- man/mseclusters.Rd | 8 man/partMat2clustVec.rd |only man/permutations.Rd |only man/relabelClusts.Rd | 7 man/uncles.Rd | 438 ++++++++++++++++++++++++++++++++++++++++-- 48 files changed, 1870 insertions(+), 95 deletions(-)
Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFieldsUtils versions 0.2.1 dated 2016-06-23 and 0.2.1.1 dated 2016-06-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/Makevars.in | 3 ++- src/options.cc | 4 ++++ src/solve.cc | 2 ++ 5 files changed, 15 insertions(+), 8 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Estimating IRT Parameters using the IRT Methodology
Description: An implementation of the IRT paradigm for the scoring of different
instruments measuring latent traits (a.k.a Abilities) and estimating item
parameters for a variety of models, this package is highly optimized using
Rcpp and carefully written R for the rest of the package, it aims to expand IRT
applications to those applications that require faster and more robust estimation
procedures. See the IRTpp documentation and github site for more information and
examples.
Author: SICS Research Group
Maintainer: Camilo Antonio Suarez Bolanos <caasuarezbo@unal.edu.co>
Diff between IRTpp versions 0.2.5 dated 2016-06-21 and 0.2.6 dated 2016-06-29
IRTpp-0.2.5/IRTpp/vignettes/Exploratory.html |only IRTpp-0.2.6/IRTpp/DESCRIPTION | 6 +-- IRTpp-0.2.6/IRTpp/MD5 | 36 +++++++++--------- IRTpp-0.2.6/IRTpp/R/models.R | 2 - IRTpp-0.2.6/IRTpp/build/vignette.rds |binary IRTpp-0.2.6/IRTpp/inst/doc/Exploratory.R |only IRTpp-0.2.6/IRTpp/inst/doc/Exploratory.Rmd |only IRTpp-0.2.6/IRTpp/inst/doc/Exploratory.html |only IRTpp-0.2.6/IRTpp/inst/irtppcpp/include/SPGO/makefile | 9 ++-- IRTpp-0.2.6/IRTpp/inst/irtppcpp/irtppcpp.mk | 8 ++-- IRTpp-0.2.6/IRTpp/inst/irtppcpp/makefile | 12 +++--- IRTpp-0.2.6/IRTpp/inst/irtppcpp/src/model/onepl.h | 2 - IRTpp-0.2.6/IRTpp/inst/irtppcpp/src/model/threepl.h | 6 +-- IRTpp-0.2.6/IRTpp/man/IRTpp-package.Rd | 2 - IRTpp-0.2.6/IRTpp/src/Makevars | 4 +- IRTpp-0.2.6/IRTpp/src/Makevars.win | 2 - IRTpp-0.2.6/IRTpp/vignettes/Exploratory.Rmd | 7 +++ IRTpp-0.2.6/IRTpp/vignettes/estimate.Rmd | 2 - IRTpp-0.2.6/IRTpp/vignettes/itemfit.Rmd | 2 - IRTpp-0.2.6/IRTpp/vignettes/parameters.Rmd | 2 - IRTpp-0.2.6/IRTpp/vignettes/simulateTest.Rmd | 2 - 21 files changed, 59 insertions(+), 45 deletions(-)
Title: Ensemble Partial Least Squares Regression
Description: An algorithmic framework for measuring feature importance, outlier detection, and ensemble modeling based on (sparse) partial least squares regressions.
Author: Nan Xiao <road2stat@gmail.com>, Dong-Sheng Cao <oriental-cds@163.com>,
Miao-Zhu Li <miaozhu.lee@gmail.com>, Qing-Song Xu <dasongxu@gmail.com>
Maintainer: Nan Xiao <road2stat@gmail.com>
Diff between enpls versions 1.1 dated 2015-11-27 and 3.0 dated 2016-06-29
enpls-1.1/enpls/NEWS |only enpls-1.1/enpls/R/enpls.en.R |only enpls-1.1/enpls/R/plot.R |only enpls-1.1/enpls/R/predict.R |only enpls-1.1/enpls/R/print.R |only enpls-1.1/enpls/inst/doc/enpls.Rnw |only enpls-1.1/enpls/inst/doc/enpls.pdf |only enpls-1.1/enpls/man/enpls.en.Rd |only enpls-1.1/enpls/man/enpls.en.core.Rd |only enpls-1.1/enpls/man/predict.enpls.en.Rd |only enpls-1.1/enpls/man/print.enpls.en.Rd |only enpls-1.1/enpls/vignettes/enpls.Rnw |only enpls-1.1/enpls/vignettes/fig |only enpls-3.0/enpls/DESCRIPTION | 19 ++--- enpls-3.0/enpls/MD5 | 104 ++++++++++++++++++------------ enpls-3.0/enpls/NAMESPACE | 42 +++++++++++- enpls-3.0/enpls/NEWS.md |only enpls-3.0/enpls/R/cv.enpls.R | 61 +++++++++-------- enpls-3.0/enpls/R/cv.enspls.R |only enpls-3.0/enpls/R/enpls-datalist.R | 44 ++++++++++-- enpls-3.0/enpls/R/enpls-package.R | 12 +-- enpls-3.0/enpls/R/enpls.fit.R |only enpls-3.0/enpls/R/enpls.fs.R | 77 +++++++++++----------- enpls-3.0/enpls/R/enpls.od.R | 73 +++++++++++---------- enpls-3.0/enpls/R/enspls.fit.R |only enpls-3.0/enpls/R/enspls.fs.R |only enpls-3.0/enpls/R/enspls.od.R |only enpls-3.0/enpls/R/plot.enpls.R |only enpls-3.0/enpls/R/plot.enspls.R |only enpls-3.0/enpls/R/predict.enpls.R |only enpls-3.0/enpls/R/predict.enspls.R |only enpls-3.0/enpls/R/print.enpls.R |only enpls-3.0/enpls/R/print.enspls.R |only enpls-3.0/enpls/README.md | 37 ++++++++-- enpls-3.0/enpls/TODO |only enpls-3.0/enpls/build/vignette.rds |binary enpls-3.0/enpls/data/logd1k.rda |only enpls-3.0/enpls/inst/doc/enpls.R | 70 ++++++++++---------- enpls-3.0/enpls/inst/doc/enpls.Rmd |only enpls-3.0/enpls/inst/doc/enpls.html |only enpls-3.0/enpls/man/alkanes.Rd | 14 ++-- enpls-3.0/enpls/man/cv.enpls.Rd | 36 ++++------ enpls-3.0/enpls/man/cv.enspls.Rd |only enpls-3.0/enpls/man/enpls-package.Rd | 14 +--- enpls-3.0/enpls/man/enpls.fit.Rd |only enpls-3.0/enpls/man/enpls.fit.core.Rd |only enpls-3.0/enpls/man/enpls.fs.Rd | 32 ++++----- enpls-3.0/enpls/man/enpls.fs.core.Rd | 2 enpls-3.0/enpls/man/enpls.od.Rd | 31 ++++---- enpls-3.0/enpls/man/enpls.od.core.Rd | 2 enpls-3.0/enpls/man/enspls.fit.Rd |only enpls-3.0/enpls/man/enspls.fit.core.Rd |only enpls-3.0/enpls/man/enspls.fs.Rd |only enpls-3.0/enpls/man/enspls.fs.core.Rd |only enpls-3.0/enpls/man/enspls.od.Rd |only enpls-3.0/enpls/man/enspls.od.core.Rd |only enpls-3.0/enpls/man/logd1k.Rd |only enpls-3.0/enpls/man/plot.cv.enpls.Rd | 30 ++++---- enpls-3.0/enpls/man/plot.cv.enspls.Rd |only enpls-3.0/enpls/man/plot.enpls.fs.Rd | 38 ++++++---- enpls-3.0/enpls/man/plot.enpls.od.Rd | 30 ++++---- enpls-3.0/enpls/man/plot.enspls.fs.Rd |only enpls-3.0/enpls/man/plot.enspls.od.Rd |only enpls-3.0/enpls/man/predict.enpls.fit.Rd |only enpls-3.0/enpls/man/predict.enspls.fit.Rd |only enpls-3.0/enpls/man/print.cv.enpls.Rd | 20 ++--- enpls-3.0/enpls/man/print.cv.enspls.Rd |only enpls-3.0/enpls/man/print.enpls.fit.Rd |only enpls-3.0/enpls/man/print.enpls.fs.Rd | 22 ++---- enpls-3.0/enpls/man/print.enpls.od.Rd | 18 ++--- enpls-3.0/enpls/man/print.enspls.fit.Rd |only enpls-3.0/enpls/man/print.enspls.fs.Rd |only enpls-3.0/enpls/man/print.enspls.od.Rd |only enpls-3.0/enpls/vignettes/enpls.Rmd |only enpls-3.0/enpls/vignettes/enpls.bib | 92 +++----------------------- enpls-3.0/enpls/vignettes/enpls.css |only enpls-3.0/enpls/vignettes/header.html |only 77 files changed, 482 insertions(+), 438 deletions(-)
Title: Estimates Pseudotimes for Single Cell Expression Data
Description: Implements the DeLorean model to estimate pseudotimes for
single cell expression data. The DeLorean model uses a Gaussian process
latent variable model to model uncertainty in the capture time of
cross-sectional data.
Author: John Reid <john.reid@mrc-bsu.cam.ac.uk>
Maintainer: John Reid <john.reid@mrc-bsu.cam.ac.uk>
Diff between DeLorean versions 1.2.2 dated 2016-05-18 and 1.2.3 dated 2016-06-29
DESCRIPTION | 13 +++--- MD5 | 28 ++++++------ NEWS.md | 11 +++-- inst/Stan/exact-sizes.stan | 53 +++++++++++------------- inst/Stan/exact.stan | 51 +++++++++++------------ inst/Stan/lowrank-sizes.stan | 78 +++++++++++++++++------------------- inst/Stan/lowrank.stan | 74 ++++++++++++++++------------------ inst/scripts/McDavid-DeLorean.Rmd | 14 +++--- inst/scripts/McDavid-Oscope.Rmd | 7 +-- inst/scripts/Shalek-DeLorean.Rmd | 34 +++++---------- inst/scripts/Windram-DeLorean.Rmd | 68 +++++++------------------------ inst/scripts/Windram-Monocle.Rmd | 5 +- inst/scripts/Windram-make-plots.Rmd | 18 ++++---- inst/scripts/config.R | 2 inst/scripts/shared.R | 27 +++++++++--- 15 files changed, 224 insertions(+), 259 deletions(-)