Title: Finding Unique or Duplicated Rows or Columns for Atomic Matrices
Description: An alternative implementation of base::duplicated.matrix(), base:anyDuplicated.matrix() and base::unique.matrix() for matrices of atomic mode, avoiding the time consuming collapse of the matrix into a character vector. An extra grpDuplicated() function is added, which groups duplicated elements together.
Author: Long Qu [aut, cre]
Maintainer: Long Qu <rtistician@gmail.com>
Diff between uniqueAtomMat versions 0.1-3-1 dated 2017-07-08 and 0.1-3-2 dated 2017-07-08
DESCRIPTION | 6 MD5 | 18 +- NAMESPACE | 32 +-- R/duplicated.matrix.R | 216 ++++++++++++------------ configure | 16 - configure.win | 16 - man/grpDuplicated.Rd | 178 ++++++++++---------- man/unique.Rd | 282 ++++++++++++++++---------------- tests/testGrpDup.R | 440 +++++++++++++++++++++++++------------------------- tests/testUnique.R | 118 ++++++------- 10 files changed, 661 insertions(+), 661 deletions(-)
Title: Survival Analysis in Health Economic Evaluation
Description: Contains a suite of functions for survival analysis in health economics. These can be used to run survival models under a frequentist (based on maximum likelihood) or a Bayesian approach (both based on Integrated Nested Laplace Approximation or Hamiltonian Monte Carlo). The user can specify a set of parametric models using a common notation and select the preferred mode of inference. The results can also be post-processed to produce probabilistic sensitivity analysis and can be used to export the output to an Excel file (e.g. for a Markov model, as often done by modellers and practitioners).
Author: Gianluca Baio
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>
Diff between survHE versions 1.0.5 dated 2017-07-01 and 1.0.6 dated 2017-07-08
DESCRIPTION | 9 - MD5 | 10 - NAMESPACE | 1 R/digitise.R | 2 inst/doc/survHE.pdf |binary src/include/models.hpp | 433 ++++++++++++++++++++++++++++--------------------- 6 files changed, 268 insertions(+), 187 deletions(-)
Title: Mixture Link Regression
Description: The Mixture Link model <arXiv:1612.03302> is a proposed extension to generalized linear models, where the outcome distribution is a finite mixture of J > 1 densities. This package supports Mixture Link computations for Poisson and Binomial outcomes. This includes the distribution functions, numerical maximum likelihood estimation, Bayesian analysis, and quantile residuals to assess model fit.
Author: Andrew M. Raim
Maintainer: Andrew M. Raim <andrew.raim@gmail.com>
Diff between mixlink versions 0.1.4 dated 2016-12-25 and 0.1.5 dated 2017-07-08
mixlink-0.1.4/mixlink/man/DIC-for-Metropolis-within-Gibbs-Sampler.Rd |only mixlink-0.1.4/mixlink/man/DIC-for-Random-Walk-Metropolis-Hastings-Sampler.Rd |only mixlink-0.1.4/mixlink/man/S3-methods-for-gibbs.mixlink.reg-output-objects.Rd |only mixlink-0.1.4/mixlink/src/MyRcppExports.cpp |only mixlink-0.1.5/mixlink/DESCRIPTION | 14 mixlink-0.1.5/mixlink/MD5 | 82 ++- mixlink-0.1.5/mixlink/NAMESPACE | 22 - mixlink-0.1.5/mixlink/R/RcppExports.R |only mixlink-0.1.5/mixlink/R/S3methods.R |only mixlink-0.1.5/mixlink/R/dist-binom.R | 11 mixlink-0.1.5/mixlink/R/dist-pois.R | 9 mixlink-0.1.5/mixlink/R/fit-mle.R | 1 mixlink-0.1.5/mixlink/R/gibbs-binom-pois.R | 112 +++-- mixlink-0.1.5/mixlink/R/metrop-binom.R | 154 ++----- mixlink-0.1.5/mixlink/R/metrop-pois.R | 70 ++- mixlink-0.1.5/mixlink/R/mixlink-package.R | 112 ++++- mixlink-0.1.5/mixlink/R/rqres.R | 8 mixlink-0.1.5/mixlink/R/rwmetrop.R | 5 mixlink-0.1.5/mixlink/R/util.R | 19 mixlink-0.1.5/mixlink/inst/examples/gibbs-binom.R | 154 +------ mixlink-0.1.5/mixlink/inst/examples/gibbs-pois.R | 87 +--- mixlink-0.1.5/mixlink/inst/examples/metrop-binom.R | 210 ---------- mixlink-0.1.5/mixlink/inst/examples/metrop-pois.R |only mixlink-0.1.5/mixlink/inst/examples/mixlink.R | 11 mixlink-0.1.5/mixlink/inst/examples/mle-binom.R | 2 mixlink-0.1.5/mixlink/inst/examples/mle-pois.R | 1 mixlink-0.1.5/mixlink/man/DIC.Rd |only mixlink-0.1.5/mixlink/man/Find-Vertices.Rd | 4 mixlink-0.1.5/mixlink/man/Metropolis-Hastings-Sampler.Rd | 24 - mixlink-0.1.5/mixlink/man/Metropolis-within-Gibbs-Sampler.Rd | 12 mixlink-0.1.5/mixlink/man/Mixture-Link-Binomial-Distribution.Rd | 5 mixlink-0.1.5/mixlink/man/Mixture-Link-Poisson-Distribution.Rd | 5 mixlink-0.1.5/mixlink/man/Numerical-MLE.Rd | 4 mixlink-0.1.5/mixlink/man/Randomized-quantile-residuals.Rd | 3 mixlink-0.1.5/mixlink/man/S3-methods-for-gibbs.mixlink-output-objects.Rd |only mixlink-0.1.5/mixlink/man/S3-methods-for-mle.fit-objects.Rd | 17 mixlink-0.1.5/mixlink/man/S3-methods-for-mle.fit.ci-objects.Rd | 1 mixlink-0.1.5/mixlink/man/S3-methods-for-rwmetrop-output-objects.Rd | 32 + mixlink-0.1.5/mixlink/man/mlogit.Rd |only mixlink-0.1.5/mixlink/man/normalize.Rd | 1 mixlink-0.1.5/mixlink/src/RcppExports.cpp |only mixlink-0.1.5/mixlink/src/density-binom.cpp | 1 mixlink-0.1.5/mixlink/src/density-pois.cpp | 1 mixlink-0.1.5/mixlink/src/find-vertices.cpp | 2 mixlink-0.1.5/mixlink/src/gibbs.cpp | 2 mixlink-0.1.5/mixlink/src/hyperg_1F1.cpp | 1 mixlink-0.1.5/mixlink/src/rwmetrop.cpp | 25 - mixlink-0.1.5/mixlink/src/util.cpp |only 48 files changed, 538 insertions(+), 686 deletions(-)
Title: Read Untidy Excel Files
Description: Imports non-tabular from Excel files into R. Exposes cell content,
position and formatting in a tidy structure for further manipulation.
Provides functions for selecting cells by position and relative position,
and for associating data cells with header cells by proximity in given
directions. Supports '.xlsx' and '.xlsm' via the embedded 'RapidXML' C++
library <http://rapidxml.sourceforge.net>. Does not support '.xlsb' or
'.xls'.
Author: Duncan Garmonsway [aut, cre],
Hadley Wickham [ctb] (Author of included readxl fragments),
RStudio [cph] (Copyright holder of included readxl fragments),
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code)
Maintainer: Duncan Garmonsway <nacnudus@gmail.com>
Diff between tidyxl versions 0.2.1 dated 2017-01-29 and 0.2.3 dated 2017-07-08
tidyxl-0.2.1/tidyxl/tests/testthat/date-bug.xlsx |only tidyxl-0.2.1/tidyxl/tests/testthat/jmp.xlsx |only tidyxl-0.2.1/tidyxl/vignettes/iris-screenshot.png |only tidyxl-0.2.3/tidyxl/DESCRIPTION | 8 tidyxl-0.2.3/tidyxl/MD5 | 83 ++--- tidyxl-0.2.3/tidyxl/NEWS.md | 24 + tidyxl-0.2.3/tidyxl/R/RcppExports.R | 4 tidyxl-0.2.3/tidyxl/R/tidy_xlsx.R | 12 tidyxl-0.2.3/tidyxl/R/utils.R | 10 tidyxl-0.2.3/tidyxl/README.md | 165 +++++----- tidyxl-0.2.3/tidyxl/build/vignette.rds |binary tidyxl-0.2.3/tidyxl/inst/doc/tidyxl.R | 10 tidyxl-0.2.3/tidyxl/inst/doc/tidyxl.Rmd | 18 - tidyxl-0.2.3/tidyxl/inst/doc/tidyxl.html | 138 ++++---- tidyxl-0.2.3/tidyxl/inst/extdata/default.xlsx |only tidyxl-0.2.3/tidyxl/man/tidy_xlsx.Rd | 6 tidyxl-0.2.3/tidyxl/src/RcppExports.cpp | 21 - tidyxl-0.2.3/tidyxl/src/color.cpp | 2 tidyxl-0.2.3/tidyxl/src/gradientFill.cpp | 8 tidyxl-0.2.3/tidyxl/src/styles.cpp | 47 +- tidyxl-0.2.3/tidyxl/src/styles.h | 3 tidyxl-0.2.3/tidyxl/src/tidyxl.cpp | 120 ++++--- tidyxl-0.2.3/tidyxl/src/utils.h | 38 ++ tidyxl-0.2.3/tidyxl/src/xf.cpp | 12 tidyxl-0.2.3/tidyxl/src/xlsxbook.cpp | 23 - tidyxl-0.2.3/tidyxl/src/xlsxbook.h | 3 tidyxl-0.2.3/tidyxl/src/xlsxcell.cpp | 41 +- tidyxl-0.2.3/tidyxl/src/xlsxcell.h | 2 tidyxl-0.2.3/tidyxl/src/xlsxsheet.cpp | 95 ++++- tidyxl-0.2.3/tidyxl/src/xlsxsheet.h | 9 tidyxl-0.2.3/tidyxl/src/zip.cpp | 7 tidyxl-0.2.3/tidyxl/src/zip.h | 3 tidyxl-0.2.3/tidyxl/tests/testthat/1900-02-29.xlsx |only tidyxl-0.2.3/tidyxl/tests/testthat/1900.xlsx |binary tidyxl-0.2.3/tidyxl/tests/testthat/comment-on-blank-cell.xlsx |only tidyxl-0.2.3/tidyxl/tests/testthat/haskell.xlsx |only tidyxl-0.2.3/tidyxl/tests/testthat/jmp-cell.xlsx |only tidyxl-0.2.3/tidyxl/tests/testthat/jmp-row.xlsx |only tidyxl-0.2.3/tidyxl/tests/testthat/libreoffice-fill.xlsx |only tidyxl-0.2.3/tidyxl/tests/testthat/libreoffice-missing-styles.xlsx |only tidyxl-0.2.3/tidyxl/tests/testthat/libreoffice_bool.xlsx |only tidyxl-0.2.3/tidyxl/tests/testthat/openxlsx1900.xlsx |only tidyxl-0.2.3/tidyxl/tests/testthat/sheet-order.xlsx |only tidyxl-0.2.3/tidyxl/tests/testthat/test-comments.R |only tidyxl-0.2.3/tidyxl/tests/testthat/test-compatibility.R | 33 +- tidyxl-0.2.3/tidyxl/tests/testthat/test-dates.R | 23 + tidyxl-0.2.3/tidyxl/tests/testthat/test-richtext.R | 10 tidyxl-0.2.3/tidyxl/tests/testthat/test-tidy_xlsx.R | 6 tidyxl-0.2.3/tidyxl/tests/testthat/utf8.xlsx |only tidyxl-0.2.3/tidyxl/vignettes/tidyxl.Rmd | 18 - tidyxl-0.2.3/tidyxl/vignettes/titanic-screenshot.png |only 51 files changed, 633 insertions(+), 369 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Multivariate linear mixed model solver for estimation of heterogeneous variances and specification of variance covariance structures. Maximum and Restricted Maximum Likelihood (ML/REML) estimates can be obtained using the Direct-Inversion Newton-Raphson (NR), Direct-Inversion Average Information (AI), MME-based Expectation-Maximization (EM), and Efficient Mixed Model Association (EMMA) algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures in R, but also functional as a regular multivariate mixed model software. Multivariate models (multiple responses) can be fitted currently with NR, AI and EMMA algorithms.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 2.8 dated 2017-06-06 and 2.9 dated 2017-07-08
CHANGELOG | 13 ++ DESCRIPTION | 10 +- MD5 | 30 +++--- R/AI.R | 112 ++++++++++++++++------ R/AImme.R | 13 ++ R/D.mat.R | 51 +++++++++- R/NR.R | 19 +++ R/blocker.R | 247 +++++++++++++++++++++++++++++++++++--------------- R/fill.design.R | 95 +++++++++++++++++-- R/mmer.R | 34 +++--- man/D.mat.Rd | 12 +- man/fill.design.Rd | 4 man/mmer.Rd | 2 man/mmer2.Rd | 2 man/sommer-package.Rd | 4 vignettes/sommer.html | 70 +++++++------- 16 files changed, 514 insertions(+), 204 deletions(-)
Title: The Scott-Knott Effect Size Difference (ESD) Test
Description: The Scott-Knott Effect Size Difference (ESD) test is a mean comparison approach that leverages a hierarchical clustering to partition the set of treatment means (e.g., means of variable importance scores, means of model performance) into statistically distinct groups with non-negligible difference [Tantithamthavorn et al., (2017) <doi:10.1109/TSE.2016.2584050>].
Author: Chakkrit Tantithamthavorn
Maintainer: Chakkrit Tantithamthavorn <kla@chakkrit.com>
Diff between ScottKnottESD versions 1.2.2 dated 2017-05-07 and 2.0.2 dated 2017-07-08
DESCRIPTION | 15 +++++++-------- MD5 | 35 +++++++++++++++++++++++------------ NAMESPACE | 9 ++++++++- R/SK.ESD.R | 2 +- R/check.ANOVA.assumptions.R | 25 +++++++++++++++---------- R/checkDifference.R |only R/example.R | 2 +- R/m.inf.1a.R |only R/maven.R |only R/normalize.R |only R/partition.R |only R/plot.sk_esd.R |only R/scottknott.R |only R/sk_esd.R | 41 ++++++++--------------------------------- R/summary.SK.R |only README.md | 36 +++++++++++++++++++++++------------- data/datalist | 3 ++- data/maven.rda |only man/ScottKnottESD-package.Rd | 34 +++++++++++++++++----------------- man/check.ANOVA.assumptions.Rd | 2 +- man/example.Rd | 2 +- man/maven.Rd |only man/normalize.Rd |only man/sk_esd.Rd | 34 ++++++++++++++++++++++------------ 24 files changed, 129 insertions(+), 111 deletions(-)
Title: Perform Two-Way Orthogonal Partial Least Squares
Description: Performs the O2PLS data integration method for two datasets yielding joint and data-specific parts for each dataset.
The algorithm automatically switches to a memory-efficient approach to fit O2PLS to high dimensional data.
It provides a rigorous and a faster alternative cross-validation method to select the number of components,
as well as functions to report proportions of explained variation and to construct plots of the results.
See Trygg and Wold (2003) <doi:10.1002/cem.775> and el Bouhaddani et al (2016) <doi:10.1186/s12859-015-0854-z>.
Author: Said el Bouhaddani, Jeanine Houwing-Duistermaat, Geurt Jongbloed, Szymon Kielbasa and
Hae-Won Uh
Maintainer: Said el Bouhaddani <s.el_bouhaddani@lumc.nl>
Diff between OmicsPLS versions 1.0.1 dated 2017-05-09 and 1.0.2 dated 2017-07-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/OmicsPLS.R | 2 +- inst/doc/OmicsPLS_vignette.pdf |binary vignettes/Figs/unnamed-chunk-2-1.pdf |binary vignettes/Figs/unnamed-chunk-5-1.pdf |binary vignettes/Figs/unnamed-chunk-5-2.pdf |binary vignettes/Figs/unnamed-chunk-6-1.pdf |binary 8 files changed, 12 insertions(+), 12 deletions(-)
Title: eXtensible Time Series
Description: Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.
Author: Jeffrey A. Ryan [aut, cph],
Joshua M. Ulrich [cre, aut],
Ross Bennett [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between xts versions 0.9-7 dated 2013-08-29 and 0.10-0 dated 2017-07-08
xts-0.10-0/xts/DESCRIPTION | 27 xts-0.10-0/xts/MD5 | 234 +++-- xts-0.10-0/xts/NAMESPACE | 78 + xts-0.10-0/xts/R/Date.R | 2 xts-0.10-0/xts/R/Math.xts.R | 2 xts-0.10-0/xts/R/OHLC.R | 2 xts-0.10-0/xts/R/Ops.xts.R | 2 xts-0.10-0/xts/R/POSIX.R | 2 xts-0.10-0/xts/R/adj.time.R | 2 xts-0.10-0/xts/R/align.time.R | 2 xts-0.10-0/xts/R/as.numeric.R | 2 xts-0.10-0/xts/R/axTicksByTime.R | 36 xts-0.10-0/xts/R/bind.R | 2 xts-0.10-0/xts/R/coredata.xts.R | 2 xts-0.10-0/xts/R/data.frame.R | 2 xts-0.10-0/xts/R/dimnames.R | 4 xts-0.10-0/xts/R/endpoints.R | 115 +- xts-0.10-0/xts/R/fillIndex.R | 2 xts-0.10-0/xts/R/first.R | 2 xts-0.10-0/xts/R/fts.R | 18 xts-0.10-0/xts/R/index.R | 89 +- xts-0.10-0/xts/R/indexClass.R | 5 xts-0.10-0/xts/R/indexFormat.R | 2 xts-0.10-0/xts/R/indexTZ.R | 16 xts-0.10-0/xts/R/irts.R | 6 xts-0.10-0/xts/R/isOrdered.R | 2 xts-0.10-0/xts/R/lag.xts.R | 15 xts-0.10-0/xts/R/last.R | 2 xts-0.10-0/xts/R/list.R | 2 xts-0.10-0/xts/R/matrix.R | 2 xts-0.10-0/xts/R/merge.R | 2 xts-0.10-0/xts/R/modify.args.R |only xts-0.10-0/xts/R/na.R | 13 xts-0.10-0/xts/R/nperiods.R | 2 xts-0.10-0/xts/R/origin.fix.R | 10 xts-0.10-0/xts/R/parse8601.R | 8 xts-0.10-0/xts/R/period.R | 2 xts-0.10-0/xts/R/periodicity.R | 14 xts-0.10-0/xts/R/plot.R | 1454 +++++++++++++++++++++++++++++++++-- xts-0.10-0/xts/R/print.R | 8 xts-0.10-0/xts/R/rollapply.xts.R | 2 xts-0.10-0/xts/R/sort.xts.R | 2 xts-0.10-0/xts/R/split.R | 22 xts-0.10-0/xts/R/start.R | 2 xts-0.10-0/xts/R/startOfYear.R | 2 xts-0.10-0/xts/R/str.R | 2 xts-0.10-0/xts/R/timeBasedRange.R | 2 xts-0.10-0/xts/R/timeBasedSeq.R | 8 xts-0.10-0/xts/R/timeDate.R | 2 xts-0.10-0/xts/R/timeSeries.R | 12 xts-0.10-0/xts/R/tis.R | 2 xts-0.10-0/xts/R/toperiod.R | 13 xts-0.10-0/xts/R/ts.R | 5 xts-0.10-0/xts/R/utils.R | 2 xts-0.10-0/xts/R/write.xts.R | 2 xts-0.10-0/xts/R/xts.R | 78 + xts-0.10-0/xts/R/xts.methods.R | 16 xts-0.10-0/xts/R/xtsible.R | 2 xts-0.10-0/xts/R/yearmon.R | 2 xts-0.10-0/xts/R/zoo.R | 2 xts-0.10-0/xts/R/zzz.R | 10 xts-0.10-0/xts/build |only xts-0.10-0/xts/inst/doc/xts-faq.R | 142 ++- xts-0.10-0/xts/inst/doc/xts-faq.Rnw |only xts-0.10-0/xts/inst/doc/xts-faq.pdf |binary xts-0.10-0/xts/inst/doc/xts.Rnw | 7 xts-0.10-0/xts/inst/doc/xts.pdf |binary xts-0.10-0/xts/inst/include/xts.h | 19 xts-0.10-0/xts/inst/include/xtsAPI.h | 40 xts-0.10-0/xts/inst/unitTests |only xts-0.10-0/xts/man/addEventLines.Rd |only xts-0.10-0/xts/man/addLegend.Rd |only xts-0.10-0/xts/man/addPanel.Rd |only xts-0.10-0/xts/man/addPolygon.Rd |only xts-0.10-0/xts/man/addSeries.Rd |only xts-0.10-0/xts/man/as.xts.Rd | 2 xts-0.10-0/xts/man/as.xts.methods.Rd | 7 xts-0.10-0/xts/man/indexTZ.Rd | 2 xts-0.10-0/xts/man/merge.Rd | 2 xts-0.10-0/xts/man/parseISO8601.Rd | 4 xts-0.10-0/xts/man/plot.xts.Rd | 173 +++- xts-0.10-0/xts/man/split.Rd | 2 xts-0.10-0/xts/man/subset.xts.Rd | 2 xts-0.10-0/xts/man/timeBasedSeq.Rd | 2 xts-0.10-0/xts/man/to.period.Rd | 2 xts-0.10-0/xts/man/xts-package.Rd | 8 xts-0.10-0/xts/man/xts.Rd | 2 xts-0.10-0/xts/src/Makevars |only xts-0.10-0/xts/src/Makevars.win |only xts-0.10-0/xts/src/attr.c | 51 - xts-0.10-0/xts/src/binsearch.c | 8 xts-0.10-0/xts/src/coredata.c | 4 xts-0.10-0/xts/src/diff.c | 319 ------- xts-0.10-0/xts/src/endpoints.c | 75 + xts-0.10-0/xts/src/extract_col.c | 85 +- xts-0.10-0/xts/src/init.c | 23 xts-0.10-0/xts/src/isOrdered.c | 2 xts-0.10-0/xts/src/isXts.c | 5 xts-0.10-0/xts/src/leadingNA.c | 251 +++++- xts-0.10-0/xts/src/merge.c | 214 ++--- xts-0.10-0/xts/src/rbind.c | 21 xts-0.10-0/xts/src/rollfun.c | 26 xts-0.10-0/xts/src/runSum.c | 11 xts-0.10-0/xts/src/startofyear.c | 2 xts-0.10-0/xts/src/subset.c | 121 ++ xts-0.10-0/xts/src/subset.old.c | 8 xts-0.10-0/xts/src/toperiod.c | 10 xts-0.10-0/xts/src/totalcols.c | 32 xts-0.10-0/xts/src/unique.time.c | 2 xts-0.10-0/xts/tests |only xts-0.10-0/xts/vignettes/xts-faq.Rnw | 277 +++--- xts-0.10-0/xts/vignettes/xts.Rnw | 7 xts-0.9-7/xts/R/barplot.xts.R |only xts-0.9-7/xts/R/its.R |only xts-0.9-7/xts/src/xts.h |only 115 files changed, 3107 insertions(+), 1245 deletions(-)
Title: Wrap R Functions for Debugging and Parametric Programming
Description: Provides 'DebugFnW()' to capture function context on error for
debugging, and 'let()' which converts non-standard evaluation interfaces to
parametric standard evaluation interfaces.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between wrapr versions 0.1.3 dated 2017-06-14 and 0.2.0 dated 2017-07-08
DESCRIPTION | 9 - MD5 | 36 ++++-- NAMESPACE | 1 NEWS.md | 7 + R/atblock.R | 67 ++++++++++++ R/let.R | 216 ++++++++++++++++++++++++++-------------- README.md | 57 +++++++++- build/vignette.rds |binary inst/doc/CornerCases.R |only inst/doc/CornerCases.Rmd |only inst/doc/CornerCases.html |only inst/doc/DebugFnW.html | 6 - inst/doc/SubstitutionModes.R |only inst/doc/SubstitutionModes.Rmd |only inst/doc/SubstitutionModes.html |only inst/doc/let.html | 4 man/ateval.Rd | 6 + man/beval.Rd | 6 + man/let.Rd | 42 ++++--- man/letprep_str.Rd | 8 - man/seval.Rd |only tests/testthat/testc.R |only vignettes/CornerCases.Rmd |only vignettes/SubstitutionModes.Rmd |only 24 files changed, 337 insertions(+), 128 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearization 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,Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). 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 0.9.4 dated 2017-05-30 and 0.9.6 dated 2017-07-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/vardannual.R | 13 ++++++------- man/vardpoor-package.Rd | 4 ++-- 4 files changed, 15 insertions(+), 16 deletions(-)
Title: Historical and Contemporary Boundaries of the United States of
America
Description: The boundaries for geographical units in the United States of
America contained in this package include state, county, congressional
district, and zip code tabulation area. Contemporary boundaries are provided
by the U.S. Census Bureau (public domain). Historical boundaries for the
years from 1629 to 2000 are provided form the Newberry Library's 'Atlas of
Historical County Boundaries' (licensed CC BY-NC-SA). Additional data is
provided in the 'USAboundariesData' package; this package provides an
interface to access that data.
Author: Lincoln Mullen [aut, cre],
Jordan Bratt [aut],
United States Census Bureau [cph]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between USAboundaries versions 0.2.0 dated 2016-01-04 and 0.3.0 dated 2017-07-08
USAboundaries-0.2.0/USAboundaries/NEWS |only USAboundaries-0.2.0/USAboundaries/R/census-bureau.R |only USAboundaries-0.2.0/USAboundaries/R/historical-atlas-county-boundaries.R |only USAboundaries-0.2.0/USAboundaries/build |only USAboundaries-0.2.0/USAboundaries/data/cb_2014_us_cd114_20m.rda |only USAboundaries-0.2.0/USAboundaries/data/cb_2014_us_county_20m.rda |only USAboundaries-0.2.0/USAboundaries/data/cb_2014_us_state_20m.rda |only USAboundaries-0.2.0/USAboundaries/data/datalist |only USAboundaries-0.2.0/USAboundaries/data/hist_us_counties.rda |only USAboundaries-0.2.0/USAboundaries/data/hist_us_states.rda |only USAboundaries-0.2.0/USAboundaries/inst |only USAboundaries-0.2.0/USAboundaries/man/census_boundaries.Rd |only USAboundaries-0.2.0/USAboundaries/man/hist_us_counties.Rd |only USAboundaries-0.2.0/USAboundaries/man/hist_us_states.Rd |only USAboundaries-0.2.0/USAboundaries/vignettes |only USAboundaries-0.3.0/USAboundaries/DESCRIPTION | 31 +-- USAboundaries-0.3.0/USAboundaries/LICENSE |only USAboundaries-0.3.0/USAboundaries/MD5 | 90 +++++----- USAboundaries-0.3.0/USAboundaries/NAMESPACE | 4 USAboundaries-0.3.0/USAboundaries/NEWS.md |only USAboundaries-0.3.0/USAboundaries/R/data-doc.R |only USAboundaries-0.3.0/USAboundaries/R/filters.R | 11 - USAboundaries-0.3.0/USAboundaries/R/install-data-pkg.R | 2 USAboundaries-0.3.0/USAboundaries/R/state_codes.R | 4 USAboundaries-0.3.0/USAboundaries/R/state_plane.R |only USAboundaries-0.3.0/USAboundaries/R/state_proj.R |only USAboundaries-0.3.0/USAboundaries/R/us_boundaries.R | 27 +-- USAboundaries-0.3.0/USAboundaries/R/us_cities.R |only USAboundaries-0.3.0/USAboundaries/R/us_congressional.R | 24 +- USAboundaries-0.3.0/USAboundaries/R/us_counties.R | 68 ++++--- USAboundaries-0.3.0/USAboundaries/R/us_states.R | 66 ++++--- USAboundaries-0.3.0/USAboundaries/R/us_zipcodes.R |only USAboundaries-0.3.0/USAboundaries/R/usboundaries-package.r | 5 USAboundaries-0.3.0/USAboundaries/README.md | 80 +++++--- USAboundaries-0.3.0/USAboundaries/data/state_proj.rda |only USAboundaries-0.3.0/USAboundaries/data/states_contemporary_lores.rda |only USAboundaries-0.3.0/USAboundaries/man/USAboundaries.Rd | 1 USAboundaries-0.3.0/USAboundaries/man/install_data_package.Rd | 1 USAboundaries-0.3.0/USAboundaries/man/state_codes.Rd | 3 USAboundaries-0.3.0/USAboundaries/man/state_plane.Rd |only USAboundaries-0.3.0/USAboundaries/man/state_proj.Rd |only USAboundaries-0.3.0/USAboundaries/man/states_contemporary_lores.Rd |only USAboundaries-0.3.0/USAboundaries/man/us_boundaries.Rd | 28 +-- USAboundaries-0.3.0/USAboundaries/man/us_cities.Rd |only USAboundaries-0.3.0/USAboundaries/man/us_congressional.Rd | 17 + USAboundaries-0.3.0/USAboundaries/man/us_counties.Rd | 52 +++-- USAboundaries-0.3.0/USAboundaries/man/us_states.Rd | 51 +++-- USAboundaries-0.3.0/USAboundaries/man/us_zipcodes.Rd |only USAboundaries-0.3.0/USAboundaries/tests/testthat.R | 8 USAboundaries-0.3.0/USAboundaries/tests/testthat/test-state_plane-standalone.R |only USAboundaries-0.3.0/USAboundaries/tests/testthat/test-us_boundaries.R | 33 +-- USAboundaries-0.3.0/USAboundaries/tests/testthat/test-us_cities.R |only USAboundaries-0.3.0/USAboundaries/tests/testthat/test-us_congressional.R | 8 USAboundaries-0.3.0/USAboundaries/tests/testthat/test-us_counties.R | 10 - USAboundaries-0.3.0/USAboundaries/tests/testthat/test-us_states-standalone.R |only USAboundaries-0.3.0/USAboundaries/tests/testthat/test-us_states.R | 10 - USAboundaries-0.3.0/USAboundaries/tests/testthat/test-us_zipcodes.R |only USAboundaries-0.3.0/USAboundaries/tools |only 58 files changed, 355 insertions(+), 279 deletions(-)
Title: Finding Unique or Duplicated Rows or Columns for Atomic Matrices
Description: An alternative implementation of base::duplicated.matrix(), base:anyDuplicated.matrix() and base::unique.matrix() for matrices of atomic mode, avoiding the time consuming collapse of the matrix into a character vector. An extra grpDuplicated() function is added, which groups duplicated elements together.
Author: Long Qu [aut, cre]
Maintainer: Long Qu <rtistician@gmail.com>
Diff between uniqueAtomMat versions 0.1-2 dated 2016-03-01 and 0.1-3-1 dated 2017-07-08
DESCRIPTION | 16 - MD5 | 22 +- NAMESPACE | 32 +-- R/duplicated.matrix.R | 216 ++++++++++++------------ configure | 16 - configure.win | 16 - man/grpDuplicated.Rd | 178 ++++++++++---------- man/unique.Rd | 282 ++++++++++++++++---------------- src/init.c | 2 src/rcSetHash.h | 12 + tests/testGrpDup.R | 440 +++++++++++++++++++++++++------------------------- tests/testUnique.R | 118 ++++++------- 12 files changed, 680 insertions(+), 670 deletions(-)
Title: 'dplyr' Functionality for Matched Tree and Data Objects
Description: Matches phylogenetic trees and trait data, and
allows simultaneous manipulation of the tree and data using 'dplyr'.
Author: Josef Uyeda
Maintainer: Josef Uyeda <josef.uyeda@gmail.com>
Diff between treeplyr versions 0.1.2 dated 2016-06-24 and 0.1.3 dated 2017-07-08
treeplyr-0.1.2/treeplyr/man/summarise_.treedata.Rd |only treeplyr-0.1.3/treeplyr/DESCRIPTION | 12 +- treeplyr-0.1.3/treeplyr/MD5 | 52 ++++---- treeplyr-0.1.3/treeplyr/NAMESPACE | 5 treeplyr-0.1.3/treeplyr/R/treeplyr-package.R | 2 treeplyr-0.1.3/treeplyr/R/treeplyr_functions.R | 125 +++++++++++++++------ treeplyr-0.1.3/treeplyr/man/anolis.Rd | 1 treeplyr-0.1.3/treeplyr/man/detectAllCharacters.Rd | 1 treeplyr-0.1.3/treeplyr/man/detectCharacterType.Rd | 1 treeplyr-0.1.3/treeplyr/man/filterMatrix.Rd | 1 treeplyr-0.1.3/treeplyr/man/filter_.treedata.Rd | 6 - treeplyr-0.1.3/treeplyr/man/forceFactor.Rd | 1 treeplyr-0.1.3/treeplyr/man/forceNames.Rd | 1 treeplyr-0.1.3/treeplyr/man/forceNumeric.Rd | 1 treeplyr-0.1.3/treeplyr/man/getVector.Rd | 1 treeplyr-0.1.3/treeplyr/man/group_by_.treedata.Rd | 7 - treeplyr-0.1.3/treeplyr/man/hasNames.Rd | 1 treeplyr-0.1.3/treeplyr/man/make.treedata.Rd | 1 treeplyr-0.1.3/treeplyr/man/mutate_.treedata.Rd | 6 - treeplyr-0.1.3/treeplyr/man/paint_clades.Rd | 1 treeplyr-0.1.3/treeplyr/man/reorder.treedata.Rd | 1 treeplyr-0.1.3/treeplyr/man/select.treedata.Rd |only treeplyr-0.1.3/treeplyr/man/select_.treedata.Rd | 7 - treeplyr-0.1.3/treeplyr/man/summarise.treedata.Rd |only treeplyr-0.1.3/treeplyr/man/tdapply.Rd | 1 treeplyr-0.1.3/treeplyr/man/treedply.treedata.Rd | 1 treeplyr-0.1.3/treeplyr/man/treeply.treedata.Rd | 1 treeplyr-0.1.3/treeplyr/man/treeplyr.Rd | 1 treeplyr-0.1.3/treeplyr/src/init.c |only 29 files changed, 138 insertions(+), 100 deletions(-)
Title: Within Outlying Mean Indexes: Refining the OMI Analysis
Description: Complementary indexes calculation to the Outlying Mean Index analysis to explore niche shift of a community and biological constraint within an Euclidean space, with graphical displays.
Author: Stephane Karasiewicz
Maintainer: Stephane Karasiewicz <stephane.karasiewicz@wanadoo.fr>
Diff between subniche versions 0.9.6 dated 2017-04-20 and 0.9.7 dated 2017-07-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/data.R | 4 ++-- R/subniche.R | 10 ++++++---- inst/CITATION | 16 ++++++++++------ man/ardecheinv.Rd | 2 +- man/drome.Rd | 2 +- man/subniche.Rd | 8 +++++--- 8 files changed, 36 insertions(+), 28 deletions(-)
Title: Tools Inspired by 'Stata' to Manipulate Tabular Data
Description: A set of tools inspired by 'Stata' to explore data.frames ('summarize',
'tabulate', 'xtile', 'pctile', 'binscatter', elapsed quarters/month, lead/lag).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mattg@princeton.edu>
Diff between statar versions 0.6.4 dated 2017-04-14 and 0.6.5 dated 2017-07-08
DESCRIPTION | 10 ++-- MD5 | 46 ++++++++++---------- NAMESPACE | 9 ---- R/fill_gap.R | 30 +++++-------- R/is.panel.R | 18 ++------ R/join.R | 42 +++++++++---------- R/pctile.R | 14 +++--- R/spread_.R | 8 --- R/statar.R | 1 R/sum_up.R | 101 ++++++++++++++++------------------------------ R/tab.R | 53 ++++-------------------- R/winsorize.R | 4 - R/xtile.R | 8 +-- inst/doc/data-frames.html | 6 +- inst/doc/graph.html | 6 +- inst/doc/panel-data.html | 6 +- inst/doc/vector.html | 6 +- man/fill_gap.Rd | 7 --- man/is.panel.Rd | 5 -- man/pctile.Rd | 4 - man/sum_up.Rd | 15 +----- man/tab.Rd | 14 +----- man/xtile.Rd | 4 - tests/testthat/test_tab.R | 5 -- 24 files changed, 149 insertions(+), 273 deletions(-)
Title: Mixed-Effect Models, Particularly Spatial Models
Description: Inference in mixed-effect models, including generalized linear mixed models with spatial
correlations and models with non-Gaussian random effects (e.g., Beta Binomial,
or negative-binomial mixed models). Variation in residual variance is handled and can be modelled
as a linear model. The algorithms are currently various Laplace approximations
methods for likelihood or restricted likelihood, in particular h-likelihood and penalized-likelihood
methods.
Author: François Rousset [aut, cre, cph],
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut],
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 2.1.0 dated 2017-05-25 and 2.1.6 dated 2017-07-08
DESCRIPTION | 8 ++--- MD5 | 29 ++++++++++----------- R/HLCor_body.R | 31 ++++++++++++++++++---- R/HLfit_Internals.R | 17 ++++++++++-- R/correlationFns.R | 2 - R/extractors.R | 8 ++--- R/fitme_body.R | 19 ++----------- R/newPLS.R | 2 - R/precision_internals.R |only R/predict.R | 37 ++++++++++++++++++++------ R/sXaug_Eigen_LDL.R | 2 - R/simulate.HL.R | 58 +++++++++++++++--------------------------- inst/NEWS.Rd | 13 +++++++++ man/predict.Rd | 11 +++---- man/simulate.HLCor.Rd | 7 +++-- tests/testthat/test-predVar.R | 4 ++ 16 files changed, 145 insertions(+), 103 deletions(-)
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like 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, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.0.0 dated 2017-06-12 and 1.0.1 dated 2017-07-08
sjlabelled-1.0.0/sjlabelled/man/var_rename.Rd |only sjlabelled-1.0.1/sjlabelled/DESCRIPTION | 18 sjlabelled-1.0.1/sjlabelled/MD5 | 33 sjlabelled-1.0.1/sjlabelled/NAMESPACE | 9 sjlabelled-1.0.1/sjlabelled/NEWS | 11 sjlabelled-1.0.1/sjlabelled/NEWS.md | 14 sjlabelled-1.0.1/sjlabelled/R/drop_labels.R | 11 sjlabelled-1.0.1/sjlabelled/R/get_model_labels.R |only sjlabelled-1.0.1/sjlabelled/R/helpfunctions.R | 38 sjlabelled-1.0.1/sjlabelled/R/read_write.R | 17 sjlabelled-1.0.1/sjlabelled/R/set_labels.R | 830 ++++++------- sjlabelled-1.0.1/sjlabelled/R/set_na.R | 2 sjlabelled-1.0.1/sjlabelled/R/to_value.R | 43 sjlabelled-1.0.1/sjlabelled/R/var_labels.R | 60 sjlabelled-1.0.1/sjlabelled/build/vignette.rds |binary sjlabelled-1.0.1/sjlabelled/inst/doc/intro_sjlabelled.html | 156 -- sjlabelled-1.0.1/sjlabelled/inst/doc/labelleddata.html | 34 sjlabelled-1.0.1/sjlabelled/man/as_numeric.Rd | 13 sjlabelled-1.0.1/sjlabelled/man/get_term_labels.Rd |only 19 files changed, 605 insertions(+), 684 deletions(-)
Title: Single Tree Simulator
Description: Forecasts plots at tree level.
Author: Clara Anton Fernandez [aut, cre],
Nikolas von Lupke [ctb]
Maintainer: Clara Anton Fernandez <caf@nibio.no>
Diff between sitree versions 0.1-1 dated 2017-03-04 and 0.1-2 dated 2017-07-08
DESCRIPTION | 8 +- MD5 | 82 ++++++++++----------- R/ManagementProb.R | 6 - R/PrepCommonVars.R | 69 +++++++++--------- R/TreeClasses.R | 2 R/dbhi.BN2009.R | 10 +- R/dev.class.R | 55 +++++++------- R/mng.tree.removal.R | 8 +- R/mort.B2007.R | 2 R/post.recover.state.R | 4 - R/recr.BBG2008.R | 6 - R/sitree.R | 57 ++++++++++----- R/sitreesummary.R | 66 ++++++++--------- R/sp.classification.R | 8 +- R/tree.age.R | 152 ++++++++++++++++++++-------------------- build/vignette.rds |binary data/StandWestSt.RData |binary data/StandWestTr.RData |binary data/fl.RData |binary data/tr.RData |binary inst/doc/TestEquations.R | 34 ++++---- inst/doc/TestEquations.Rmd | 36 ++++----- inst/doc/TestEquations.html | 50 ++++++------- man/dbhi.BN2009.Rd | 8 +- man/fl.Rd | 2 man/grow.dbhinc.hgtinc.Rd | 8 +- man/height.korf.Rd | 8 +- man/management.prob.Rd | 8 +- man/mng.tree.removal.Rd | 10 +- man/mort.B2007.Rd | 8 +- man/prep.common.vars.fun.Rd | 8 +- man/recover.last.measurement.Rd | 6 - man/recr.BBG2008.Rd | 8 +- man/sitree.Rd | 16 ++-- man/sitreesummary.Rd | 6 - man/sp.classification.Rd | 18 ++-- man/stand.west.st.Rd | 2 man/stand.west.tr.Rd | 2 man/tr.Rd | 2 man/trList-class.Rd | 2 man/tree.age.Rd | 6 - vignettes/TestEquations.Rmd | 36 ++++----- 42 files changed, 428 insertions(+), 391 deletions(-)
Title: Simulation Education
Description: Contains various functions to be used for simulation education,
including queueing simulation functions, variate generation functions
capable of producing independent streams and antithetic variates, functions
for illustrating random variate generation for various discrete and
continuous distributions, and functions to compute time-persistent
statistics. Also contains two queueing data sets (one fabricated, one
real-world) to facilitate input modeling.
Author: Barry Lawson, Larry Leemis
Maintainer: Barry Lawson <blawson@richmond.edu>
Diff between simEd versions 1.0.1 dated 2017-05-23 and 1.0.2 dated 2017-07-08
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------- NEWS.md | 9 ++++++ R/inorm.R | 2 - R/iunif.R | 2 - README.md | 4 +-- build/partial.rdb |binary man/msq.Rd | 41 +++++++++++++++++++++++++++++++ man/simEd-package.Rd | 4 +-- man/ssq.Rd | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++ 10 files changed, 134 insertions(+), 18 deletions(-)
Title: Format Significance Summaries for Reports
Description: Succinctly format significance summaries of
various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). The main purpose is unified reporting and planning
of experimental results, working around issue such as the difficulty of
extracting model summary facts (such as with 'lm'/'glm'). This package also
includes empirical tests, such as bootstrap estimates.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between sigr versions 0.1.6 dated 2017-05-05 and 0.1.7 dated 2017-07-08
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/ChiSqTest.R | 2 +- build/vignette.rds |binary inst/doc/lmExample.html | 4 ++-- inst/doc/sigrFormatting.html | 6 ++---- 7 files changed, 20 insertions(+), 17 deletions(-)
Title: Implement Material Design in Shiny Applications
Description: Allows shiny developers to incorporate UI elements based on Google's Material design. See <https://material.io/guidelines/> for more information.
Author: Eric Anderson [aut, cre],
Alvin Wang [ctb, cph] (Materialize CSS library),
Alan Chang [ctb, cph] (Materialize CSS library),
Alex Mark [ctb, cph] (Materialize CSS library),
Kevin Louie [ctb, cph] (Materialize CSS library)
Maintainer: Eric Anderson <eric.ray.anderson@gmail.com>
Diff between shinymaterial versions 0.2.1 dated 2017-04-29 and 0.3.0 dated 2017-07-08
DESCRIPTION | 6 ++-- MD5 | 42 +++++++++++++++++---------------- R/shiny-material-checkbox.R | 2 - R/shiny-material-dropdown.R | 2 - R/shiny-material-number-box.R | 14 +++++------ R/shiny-material-page.R | 12 ++++++--- R/shiny-material-password-box.R | 14 +++++------ R/shiny-material-radio-button.R | 4 +-- R/shiny-material-switch.R | 12 ++++----- R/shiny-material-text-box.R | 14 +++++------ inst/css/shiny-material-page.css | 4 +++ inst/doc/shinymaterial.pdf |binary inst/js/shiny-material-dropdown.js | 2 - inst/js/shiny-material-page.js |only inst/js/shiny-material-radio-button.js | 2 - man/material_checkbox.Rd | 2 - man/material_number_box.Rd | 10 +++++++ man/material_page.Rd | 6 ++-- man/material_password_box.Rd | 7 +++++ man/material_switch.Rd | 14 +++++++++-- man/material_text_box.Rd | 7 +++++ tests/app.R | 8 +++--- tests/github.R |only 23 files changed, 114 insertions(+), 70 deletions(-)
Title: Import XY-Data into R
Description: Provides access to the 'xylib' C library for to import xy
data from powder diffraction, spectroscopy and other experimental methods.
Author: Sebastian Kreutzer [aut, trl, cre],
Johannes Friedrich [ctb],
RLum Team [ctb],
Marcin Wojdyr [cph] (C++ library 'xylib'),
Peng Zhang [cph] (C++ library 'xylib')
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between rxylib versions 0.1.0 dated 2017-06-30 and 0.1.1 dated 2017-07-08
DESCRIPTION | 12 +++++++----- MD5 | 38 +++++++++++++++++++++----------------- NEWS | 9 +++++++++ R/RcppExports.R | 4 ++-- R/read_xyData.R | 26 +++++++++++++++----------- R/rxylib.R | 4 ++-- inst/include/xylib/bruker_spc.h |only inst/include/xylib/util.h | 19 +++++++++++++------ inst/include/xylib/xsyg.h |only inst/include/xylib/xylib.h | 5 +---- man/read_xyData.Rd | 2 +- man/rxylib-package.Rd | 25 ++----------------------- src/Makevars | 2 ++ src/get_supportedFormats.cpp | 4 ++-- src/read_data.cpp | 1 + src/xylib/bruker_spc.cpp |only src/xylib/pdcif.cpp | 10 +++++----- src/xylib/util.cpp | 22 +++++++++++++++++----- src/xylib/winspec_spe.cpp | 5 ++--- src/xylib/xsyg.cpp |only src/xylib/xylib.cpp | 6 +++++- tests/testthat/test_read_xyData.R | 17 +++++++++++------ 22 files changed, 118 insertions(+), 93 deletions(-)
Title: Analyse Sentiment of English Sentences
Description: Analyses sentiment of a sentence in English and assigns score to it. It can classify sentences to the following categories of sentiments:- Positive, Negative, very Positive, very negative,
Neutral. For a vector of sentences, it counts the number of sentences in each
category of sentiment.In calculating the score, negation and various degrees
of adjectives are taken into consideration. It deals only with English sentences.
Author: Subhasree Bose <subhasree10.7@gmail.com> with contributons from Saptarsi Goswami.
Maintainer: Subhasree Bose <subhasree10.7@gmail.com>
Diff between RSentiment versions 2.1.4 dated 2017-06-10 and 2.1.5 dated 2017-07-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/test.R | 18 +++++++++--------- 3 files changed, 15 insertions(+), 15 deletions(-)
Title: Fast Simulation of Normal/Exponential Random Variables and
Stochastic Differential Equations / Poisson Processes
Description: Fast simulation of some random variables than the usual native functions, including rnorm() and rexp(), using Ziggurat method, reference: MARSAGLIA, George, TSANG, Wai Wan, and al. (2000) <doi:10.18637/jss.v005.i08>, and fast simulation of stochastic differential equations / Poisson processes.
Author: Nicolas Baradel
Maintainer: Nicolas Baradel - PGM Solutions <nicolas.baradel@pgm-solutions.com>
Diff between rpgm versions 1.0.0 dated 2017-03-16 and 1.0.1 dated 2017-07-08
DESCRIPTION | 12 +-- MD5 | 83 +++++++++++++------------ NAMESPACE | 7 +- R/bound.R | 24 +++---- R/jarquebera.R | 8 +- R/kurtosis.R | 10 +-- R/onLoad.R | 10 +-- R/rbernou.R | 10 +-- R/rbrownian.R | 10 +-- R/rcantor.R | 10 +-- R/reuleur.R | 48 +++++++------- R/rgpd.R | 10 +-- R/rmilstein.R | 56 ++++++++--------- R/rowMaxs.R | 98 ++++++++++++++--------------- R/rpgm.rexp.R | 10 +-- R/rpgm.rgeom.R | 10 +-- R/rpgm.rlnorm.R | 10 +-- R/rpgm.rnorm.R | 10 +-- R/rpgm.rt.R | 10 +-- R/rpoisson.R |only R/rvasicek.R | 94 ++++++++++++++-------------- R/skewness.R | 10 +-- man/bound.Rd | 108 ++++++++++++++++----------------- man/colMaxs.Rd | 100 +++++++++++++++--------------- man/jarquebera.Rd | 100 +++++++++++++++--------------- man/kurtosis.Rd | 100 +++++++++++++++--------------- man/rbernou.Rd | 98 ++++++++++++++--------------- man/rbrownian.Rd | 122 ++++++++++++++++++------------------- man/rcantor.Rd | 92 ++++++++++++++-------------- man/reuler.Rd | 144 ++++++++++++++++++++++---------------------- man/revalpoisson.Rd |only man/rgpd.Rd | 114 +++++++++++++++++----------------- man/rinpoisson.Rd |only man/rmilstein.Rd | 152 +++++++++++++++++++++++----------------------- man/rpgm-package.Rd | 64 +++++++++---------- man/rpgm.rexp.Rd | 98 ++++++++++++++--------------- man/rpgm.rgeom.Rd | 98 ++++++++++++++--------------- man/rpgm.rlnorm.Rd | 104 +++++++++++++++---------------- man/rpgm.rnorm.Rd | 104 +++++++++++++++---------------- man/rpgm.rt.Rd | 98 ++++++++++++++--------------- man/rpoisson.Rd |only man/rvasicek.Rd | 170 ++++++++++++++++++++++++++-------------------------- man/skewness.Rd | 100 +++++++++++++++--------------- src/rpgm_init.c | 7 ++ src/rpoisson.c |only 45 files changed, 1268 insertions(+), 1255 deletions(-)
Title: Robust Rank Correlation Coefficient and Test
Description: The 'rococo' package provides a robust gamma rank correlation
coefficient along with a permutation-based rank correlation test.
The rank correlation coefficient and the test are explicitly
designed for dealing with noisy numerical data.
Author: Martin Krone, Ulrich Bodenhofer
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Diff between rococo versions 1.1.4 dated 2016-10-07 and 1.1.5 dated 2017-07-08
rococo-1.1.4/rococo/src/rcor_sum.cpp |only rococo-1.1.4/rococo/src/rcor_sum.h |only rococo-1.1.5/rococo/DESCRIPTION | 8 rococo-1.1.5/rococo/MD5 | 29 - rococo-1.1.5/rococo/R/rococo.R | 93 ++- rococo-1.1.5/rococo/R/rococo.test-methods.R | 696 +++++++++++++++------------- rococo-1.1.5/rococo/build/vignette.rds |binary rococo-1.1.5/rococo/inst/NEWS | 4 rococo-1.1.5/rococo/inst/doc/rococo.Rnw | 5 rococo-1.1.5/rococo/inst/doc/rococo.pdf |binary rococo-1.1.5/rococo/src/R_init_rococo.cpp |only rococo-1.1.5/rococo/src/rcor.cpp | 43 - rococo-1.1.5/rococo/src/rcor.h | 2 rococo-1.1.5/rococo/src/rcor_exacttest.cpp | 41 - rococo-1.1.5/rococo/src/rcor_exacttest.h |only rococo-1.1.5/rococo/src/rcor_permtest.cpp | 42 - rococo-1.1.5/rococo/src/rcor_permtest.h |only rococo-1.1.5/rococo/vignettes/rococo.Rnw | 5 18 files changed, 524 insertions(+), 444 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: A 'DBI' interface to 'MySQL' / 'MariaDB'. The 'RMySQL' package contains an
old implementation based on legacy code from S-PLUS which being phased out. A modern
'MySQL' client based on 'Rcpp' is available from the 'RMariaDB' package on 'Github':
<https://github.com/rstats-db/RMariaDB>.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between RMySQL versions 0.10.11 dated 2017-03-29 and 0.10.12 dated 2017-07-08
RMySQL-0.10.11/RMySQL/README.md |only RMySQL-0.10.12/RMySQL/DESCRIPTION | 13 +++++++------ RMySQL-0.10.12/RMySQL/MD5 | 11 +++++------ RMySQL-0.10.12/RMySQL/NEWS.md | 4 ++++ RMySQL-0.10.12/RMySQL/configure | 4 ++++ RMySQL-0.10.12/RMySQL/src/Makevars.win | 4 ++-- RMySQL-0.10.12/RMySQL/tools/winlibs.R | 5 ++--- 7 files changed, 24 insertions(+), 17 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of MUMPS (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis,
LU (or LDL^t) factorization and system solving.
Author: Serguei Sokol
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.1.1-1 dated 2017-04-26 and 5.1.1-2 dated 2017-07-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 9 ++++++++- man/rmumps-package.Rd | 2 +- src/lib/MUMPS_5.1.1/src/dana_aux_ELT.F | 3 ++- src/lib/MUMPS_5.1.1/src/dana_aux_par.F | 5 +++-- src/lib/MUMPS_5.1.1/src/mumps_save_restore_C.h | 2 +- 7 files changed, 25 insertions(+), 16 deletions(-)
Title: Wrapper for the 'Intro.js' Library
Description: A wrapper for the 'Intro.js' library (For more info: <http://www.introjs.com>).
This package makes it easy to include step-by-step introductions, and clickable hints in a 'Shiny'
application. It supports both static introductions in the UI, and programmatic introductions from
the server-side.
Author: Carl Ganz [aut, cre],
Afshin Mehrabani [ctb, cph] (intro.js in javascript/introjs)
Maintainer: Carl Ganz <carlganz@gmail.com>
Diff between rintrojs versions 0.1.2 dated 2016-12-02 and 0.2.0 dated 2017-07-08
DESCRIPTION | 8 - MD5 | 18 ++-- NEWS.md | 14 +++ R/introjs.R | 134 ++++++++++++++++++++------------ README.md | 8 + inst/javascript/introjs/intro.min.js | 95 ++++++++++++---------- inst/javascript/introjs/introjs.min.css | 2 man/introBox.Rd | 9 +- man/introjs.Rd | 7 - man/introjsUI.Rd | 7 + 10 files changed, 183 insertions(+), 119 deletions(-)
Title: Diligent Use of Big Data for R
Description: Methods to diligently use 'dplyr' remote data sources ('SQL' databases,
'Spark' 2.0.0 and above).
Adds convenience functions to make such tasks more like
working with an in-memory R 'data.frame'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between replyr versions 0.4.0 dated 2017-06-12 and 0.4.2 dated 2017-07-08
replyr-0.4.0/replyr/man/tableDesription.Rd |only replyr-0.4.2/replyr/DESCRIPTION | 12 replyr-0.4.2/replyr/MD5 | 86 - replyr-0.4.2/replyr/NAMESPACE | 10 replyr-0.4.2/replyr/NEWS.md | 6 replyr-0.4.2/replyr/R/addCol.R | 2 replyr-0.4.2/replyr/R/bind_rows.R | 196 ++- replyr-0.4.2/replyr/R/coalesce.R | 4 replyr-0.4.2/replyr/R/copyToFrom.R | 10 replyr-0.4.2/replyr/R/joinController.R | 742 +++++++++++++-- replyr-0.4.2/replyr/R/land.R | 2 replyr-0.4.2/replyr/R/nrow.R | 55 - replyr-0.4.2/replyr/R/renameRestrictCols.R | 6 replyr-0.4.2/replyr/R/summary.R | 2 replyr-0.4.2/replyr/R/tempNameGenerator.R | 34 replyr-0.4.2/replyr/R/underscoreReplacements.R | 7 replyr-0.4.2/replyr/README.md | 11 replyr-0.4.2/replyr/build/vignette.rds |binary replyr-0.4.2/replyr/inst/doc/BizarroPipe.html | 4 replyr-0.4.2/replyr/inst/doc/DependencySorting.R |only replyr-0.4.2/replyr/inst/doc/DependencySorting.Rmd |only replyr-0.4.2/replyr/inst/doc/DependencySorting.html |only replyr-0.4.2/replyr/inst/doc/NArm.html | 20 replyr-0.4.2/replyr/inst/doc/ParametricExample.html | 6 replyr-0.4.2/replyr/inst/doc/coalesce.html | 16 replyr-0.4.2/replyr/inst/doc/joinController.R | 79 + replyr-0.4.2/replyr/inst/doc/joinController.Rmd | 121 +- replyr-0.4.2/replyr/inst/doc/joinController.html | 232 ++-- replyr-0.4.2/replyr/inst/doc/letExample.html | 8 replyr-0.4.2/replyr/inst/doc/replyr.html | 15 replyr-0.4.2/replyr/inst/doc/summary.html | 11 replyr-0.4.2/replyr/man/buildJoinPlan.Rd | 17 replyr-0.4.2/replyr/man/convertDiagrameToPNG.Rd |only replyr-0.4.2/replyr/man/executeLeftJoinPlan.Rd | 23 replyr-0.4.2/replyr/man/inspectDescrAndJoinPlan.Rd | 13 replyr-0.4.2/replyr/man/key_inspector_all_cols.Rd |only replyr-0.4.2/replyr/man/key_inspector_postgresql.Rd |only replyr-0.4.2/replyr/man/key_inspector_sqlite.Rd |only replyr-0.4.2/replyr/man/keysAreUnique.Rd | 9 replyr-0.4.2/replyr/man/makeJoinDiagramSpec.Rd |only replyr-0.4.2/replyr/man/makeTempNameGenerator.Rd | 12 replyr-0.4.2/replyr/man/renderJoinDiagram.Rd |only replyr-0.4.2/replyr/man/replyr_bind_rows.Rd | 16 replyr-0.4.2/replyr/man/replyr_copy_to.Rd | 4 replyr-0.4.2/replyr/man/replyr_hasrows.Rd |only replyr-0.4.2/replyr/man/replyr_union_all.Rd | 15 replyr-0.4.2/replyr/man/tableDescription.Rd |only replyr-0.4.2/replyr/man/topoSortTables.Rd |only replyr-0.4.2/replyr/tests/testthat/test_replyr_copy_to.R | 5 replyr-0.4.2/replyr/vignettes/DependencySorting.Rmd |only replyr-0.4.2/replyr/vignettes/joinController.Rmd | 121 +- 51 files changed, 1456 insertions(+), 476 deletions(-)
Title: Diagnostics to Assess the Effects of Text Preprocessing
Decisions
Description: Functions to assess the effects of different text preprocessing decisions on the inferences drawn from the resulting document-term matrices they generate.
Author: Matthew J. Denny <mdenny@psu.edu>, Arthur Spirling
<as9934@nyu.edu>,
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between preText versions 0.5.0 dated 2017-05-26 and 0.6.0 dated 2017-07-08
DESCRIPTION | 8 - MD5 | 20 +- R/parallel_preprocess.R | 197 ++++++++++++++++++++++++----- R/preText.R | 5 R/scaling_comparison.R | 95 ++++++++----- R/zzz.R | 4 README.md | 2 build/vignette.rds |binary data/UK_Manifestos.rda |binary inst/doc/getting_started_with_preText.html | 12 - man/scaling_comparison.Rd | 4 11 files changed, 255 insertions(+), 92 deletions(-)
Title: R Markdown Templates to Preregister Scientific Studies
Description: Provides a collection of templates to author preregistration documents for scientific studies in PDF format.
Author: Frederik Aust [aut, cre]
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>
Diff between prereg versions 0.2.0 dated 2016-09-20 and 0.3.0 dated 2017-07-08
prereg-0.2.0/prereg/NEWS.md |only prereg-0.2.0/prereg/inst/rmarkdown/templates/aspredicted_prereg/resources |only prereg-0.2.0/prereg/inst/rmarkdown/templates/cos_prereg/resources |only prereg-0.3.0/prereg/DESCRIPTION | 15 +-- prereg-0.3.0/prereg/MD5 | 46 ++++++---- prereg-0.3.0/prereg/NAMESPACE | 2 prereg-0.3.0/prereg/R/aspredicted_prereg.R | 43 --------- prereg-0.3.0/prereg/R/brandt_prereg.R |only prereg-0.3.0/prereg/R/cos_prereg.R | 44 --------- prereg-0.3.0/prereg/R/prereg.R | 13 +- prereg-0.3.0/prereg/R/utils.R |only prereg-0.3.0/prereg/R/vantveer_prereg.R |only prereg-0.3.0/prereg/README.md | 25 +++-- prereg-0.3.0/prereg/inst/NEWS.md |only prereg-0.3.0/prereg/inst/rmarkdown/templates/aspredicted_prereg/template.yaml | 4 prereg-0.3.0/prereg/inst/rmarkdown/templates/brandt_prereg |only prereg-0.3.0/prereg/inst/rmarkdown/templates/cos_prereg/template.yaml | 4 prereg-0.3.0/prereg/inst/rmarkdown/templates/vantveer_prereg |only prereg-0.3.0/prereg/inst/rmd |only prereg-0.3.0/prereg/man/aspredicted_prereg.Rd | 1 prereg-0.3.0/prereg/man/brandt_prereg.Rd |only prereg-0.3.0/prereg/man/cos_prereg.Rd | 1 prereg-0.3.0/prereg/man/prereg.Rd | 14 ++- prereg-0.3.0/prereg/man/vantveer_prereg.Rd |only prereg-0.3.0/prereg/tests/testthat/test_skeletons.R | 40 ++++++++ prereg-0.3.0/prereg/tools |only 26 files changed, 120 insertions(+), 132 deletions(-)
Title: Parses Web Pages using Postlight Mercury
Description: This is a wrapper for the Mercury Parser API. The Mercury Parser is
a single API endpoint that takes a URL and gives you back the content reliably
and easily.
With just one API request, Mercury takes any web article and returns
only the relevant content — headline, author, body text, relevant images and
more — free from any clutter. It’s reliable, easy-to-use and free.
See the webpage here: <https://mercury.postlight.com/>.
Author: Mikkel Freltoft Krogsholm
Maintainer: Mikkel Freltoft Krogsholm <mikkel@56n.dk>
Diff between postlightmercury versions 1.0 dated 2017-06-26 and 1.1 dated 2017-07-08
DESCRIPTION | 10 ++++----- MD5 | 8 ++++--- NEWS.md |only R/mercury.R | 60 +++++++++++++++++++++++++++++++++--------------------- README.md | 23 +------------------- man/null_to_na.Rd |only 6 files changed, 49 insertions(+), 52 deletions(-)
More information about postlightmercury at CRAN
Permanent link
Title: Graphing Nonlinear Relations Among Latent Variables from
Structural Equation Mixture Models
Description: Contains a graphical user interface to generate the diagnostic
plots proposed by Bauer (2005; <doi:10.1207/s15328007sem1204_1>),
Pek & Chalmers (2015; <doi:10.1080/10705511.2014.937790>), and
Pek, Chalmers, R. Kok, & Losardo (2015; <doi:10.3102/1076998615589129>) to investigate
nonlinear bivariate relationships in latent regression models using structural
equation mixture models (SEMMs).
Author: Bethany Kok [aut],
Jolynn Pek [aut],
Sonya Sterba [ctb],
Dan Bauer [ctb],
Phil Chalmers [cre, aut]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between plotSEMM versions 2.2 dated 2016-05-24 and 2.4 dated 2017-07-08
DESCRIPTION | 13 +++++++------ MD5 | 27 ++++++++++++++------------- R/plotSEMM-package.R | 8 ++++++++ R/plotSEMM_GUI.R | 4 ++-- R/plotSEMM_contour.R | 8 ++++++++ R/plotSEMM_probability.R | 8 ++++++++ R/plotSEMM_setup.R | 8 ++++++++ README.md | 2 ++ build |only man/plotSEMM.Rd | 10 +++++++++- man/plotSEMM_GUI.Rd | 11 +++++------ man/plotSEMM_contour.Rd | 10 +++++++++- man/plotSEMM_probability.Rd | 14 +++++++++++--- man/plotSEMM_setup.Rd | 14 +++++++++++--- src/linear.cpp | 6 ++++++ 15 files changed, 108 insertions(+), 35 deletions(-)
Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory
phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
(2012) <doi:10.1111/j.1558-5646.2012.01790.x>.
Author: Wouter van der Bijl [aut, cre]
Maintainer: Wouter van der Bijl <wouter.van.der.bijl@zoologi.su.se>
Diff between phylopath versions 0.2.3 dated 2017-03-23 and 0.3.0 dated 2017-07-08
phylopath-0.2.3/phylopath/vignettes/Vignette_figures |only phylopath-0.3.0/phylopath/DESCRIPTION | 19 - phylopath-0.3.0/phylopath/MD5 | 57 ++- phylopath-0.3.0/phylopath/NAMESPACE | 11 phylopath-0.3.0/phylopath/NEWS.md | 20 + phylopath-0.3.0/phylopath/R/DAG.R | 43 ++ phylopath-0.3.0/phylopath/R/data_docs.R | 35 +- phylopath-0.3.0/phylopath/R/internal.R | 98 +++++- phylopath-0.3.0/phylopath/R/phylopath.R | 193 +++++++++--- phylopath-0.3.0/phylopath/R/print_and_plot.R | 205 ++++++++++--- phylopath-0.3.0/phylopath/R/sysdata.rda |only phylopath-0.3.0/phylopath/build/vignette.rds |binary phylopath-0.3.0/phylopath/data/cichlids.rda |only phylopath-0.3.0/phylopath/data/cichlids_tree.rda |only phylopath-0.3.0/phylopath/inst/doc/binary_models.R |only phylopath-0.3.0/phylopath/inst/doc/binary_models.Rmd |only phylopath-0.3.0/phylopath/inst/doc/binary_models.html |only phylopath-0.3.0/phylopath/inst/doc/intro_to_phylopath.R | 29 - phylopath-0.3.0/phylopath/inst/doc/intro_to_phylopath.Rmd | 32 -- phylopath-0.3.0/phylopath/inst/doc/intro_to_phylopath.html | 75 ++-- phylopath-0.3.0/phylopath/man/average.Rd | 23 + phylopath-0.3.0/phylopath/man/average_DAGs.Rd | 6 phylopath-0.3.0/phylopath/man/cichlids.Rd |only phylopath-0.3.0/phylopath/man/cichlids_tree.Rd |only phylopath-0.3.0/phylopath/man/est_DAG.Rd | 2 phylopath-0.3.0/phylopath/man/est_DAG_binary.Rd |only phylopath-0.3.0/phylopath/man/phylo_path.Rd | 5 phylopath-0.3.0/phylopath/man/phylo_path_binary.Rd |only phylopath-0.3.0/phylopath/man/plot.DAG.Rd |only phylopath-0.3.0/phylopath/man/plot.fitted_DAG.Rd |only phylopath-0.3.0/phylopath/man/plot_model_set.Rd |only phylopath-0.3.0/phylopath/man/reexports.Rd |only phylopath-0.3.0/phylopath/man/rhino.Rd | 6 phylopath-0.3.0/phylopath/man/rhino_tree.Rd | 6 phylopath-0.3.0/phylopath/vignettes/binary_models.Rmd |only phylopath-0.3.0/phylopath/vignettes/intro_to_phylopath.Rmd | 32 -- 36 files changed, 662 insertions(+), 235 deletions(-)
Title: Multivariate Analysis of Mixed Data
Description: Principal Component Analysis, orthogonal rotation and multiple
factor analysis for a mixture of quantitative and qualitative variables.
Author: Marie Chavent [aut, cre],
Vanessa Kuentz [aut],
Amaury Labenne [aut],
Benoit Liquet [aut],
Jerome Saracco [aut]
Maintainer: Marie Chavent <Marie.Chavent@u-bordeaux.fr>
Diff between PCAmixdata versions 2.2 dated 2014-12-05 and 3.0 dated 2017-07-08
DESCRIPTION | 26 MD5 | 85 +- NAMESPACE | 34 - R/Lg.R | 60 -- R/Lg.pond.R | 33 - R/MFAmix.R | 394 +++++-------- R/PCAmix.R | 537 +++++++++-------- R/PCArot.R | 243 ++++---- R/RV.R | 1 R/RV.pond.R | 1 R/nb.level.R | 1 R/plot.MFAmix.R | 1498 +++++++++++++++++++++++++++----------------------- R/plot.PCAmix.R | 890 ++++++++++++++++------------- R/predict.MFAmix.R | 146 +++- R/predict.PCAmix.R | 108 ++- R/print.MFAmix.R | 21 R/print.PCAmix.R | 88 +- R/recod.R | 25 R/recodqual.R | 3 R/recodquant.R | 3 R/sol.2dim.R | 1 R/splitgroups.R | 20 R/splitmix.R | 38 - R/summary.MFAmix.R | 2 R/summary.PCAmix.R | 2 R/supvar.MFAmix.R |only R/supvar.PCAmix.R |only R/svd.triplet.R | 1 R/tab.disjonctif.NA.R | 2 README.md |only data/dogs.RData |only data/protein.RData |only inst |only man/Lg.Rd | 21 man/Lg.pond.Rd | 26 man/MFAmix.Rd | 21 man/PCAmix.Rd | 210 +++---- man/PCArot.Rd | 8 man/dogs.Rd |only man/plot.MFAmix.Rd | 244 ++++---- man/plot.PCAmix.Rd | 178 +++-- man/predict.MFAmix.Rd | 91 +-- man/predict.PCAmix.Rd | 79 +- man/protein.Rd |only man/splitgroups.Rd | 16 man/splitmix.Rd | 6 man/supvar.MFAmix.Rd |only man/supvar.PCAmix.Rd |only man/supvar.Rd |only 49 files changed, 2809 insertions(+), 2354 deletions(-)
Title: Additive Partitions of Integers
Description: Additive partitions of integers. Enumerates the
partitions, unequal partitions, and restricted partitions of an
integer; the three corresponding partition functions are also
given. Set partitions are now included.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between partitions versions 1.9-18 dated 2015-08-06 and 1.9-19 dated 2017-07-08
DESCRIPTION |only MD5 |only NAMESPACE |only R |only build |only inst/doc/partitionspaper.R |only inst/doc/partitionspaper.pdf |binary inst/doc/scrabble.R |only inst/doc/scrabble.pdf |binary inst/doc/setpartitions.pdf |binary man |only src |only tests |only vignettes |only 14 files changed
Title: Tools for Analysing UK Politics
Description: Provides various tools for analysing UK political data, including creating political cartograms and retrieving data.
Author: Evan Odell [aut, cre]
Maintainer: Evan Odell <evanodell91@gmail.com>
Diff between parlitools versions 0.0.4 dated 2017-06-05 and 0.0.7 dated 2017-07-08
DESCRIPTION | 10 +- MD5 | 50 +++++++------- R/current_mps.R | 49 ++++++++------ R/data.R | 42 ++++++++++-- R/mps_on_date.R | 28 ++++++-- R/parlitools_tidy.R | 8 -- build/vignette.rds |binary data/datalist | 1 data/leave_votes_west.rda |only data/west_hex_map.rda |binary inst/doc/bes-2015.html | 4 - inst/doc/introduction.R | 34 ++++++++- inst/doc/introduction.Rmd | 98 +++++++++++++++++++++++++--- inst/doc/introduction.html | 111 ++++++++++++++++++++++++++------ inst/doc/mapping-local-authorities.html | 8 +- inst/doc/using-cartograms.html | 12 +-- man/bes_2015.Rd | 9 +- man/council_data.Rd | 4 - man/current_mps.Rd | 4 - man/leave_votes_west.Rd |only man/local_hex_map.Rd | 4 - man/party_colour.Rd | 4 - man/west_hex_map.Rd | 4 - tests/testthat/test_current_mps.R | 10 +- tests/testthat/test_mps_on_date.R | 2 tools/hex_map.png |binary vignettes/introduction.Rmd | 98 +++++++++++++++++++++++++--- 27 files changed, 454 insertions(+), 140 deletions(-)
Title: Orthogonalizing EM
Description: Solves penalized least squares problems for big tall data
using the orthogonalizing EM algorithm of Xiong et al. (2016) <doi:
10.1080/00401706.2015.1054436>. The main fitting function is oem() and the
functions cv.oem() and xval.oem() are for cross validation, the latter being an
accelerated cross validation function for linear models. The big.oem() function
allows for out of memory fitting.
Author: Bin Dai [aut],
Jared Huling [aut, cre],
Yixuan Qiu [ctb]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between oem versions 2.0.5 dated 2017-03-22 and 2.0.6 dated 2017-07-08
DESCRIPTION | 17 ++-- MD5 | 84 ++++++++++---------- R/big_oem.R | 48 +++++++++-- R/cv_oem.R | 184 ++++++++++++++++++++++++-------------------- R/methods.R | 31 +++---- R/oem.R | 62 ++++++++++++-- R/oem_xtx.R | 48 +++++++++-- R/oem_xval.R | 48 +++++++++-- R/utils.R | 6 - README.md | 103 ++++++++++-------------- build/vignette.rds |binary inst/doc/oem_vignette.Rmd | 6 - inst/doc/oem_vignette.html | 60 +++++++------- man/big.oem.Rd | 3 man/cv.oem.Rd | 1 man/deprecated.Rd | 5 - man/logLik.Rd | 3 man/oem.Rd | 9 +- man/oem.xtx.Rd | 3 man/plot.Rd | 3 man/predict.cv.oem.Rd | 1 man/predict.oem.Rd | 1 man/predict.xval.oem.Rd | 1 man/print.Rd | 1 man/summary.Rd | 1 man/xval.oem.Rd | 3 src/oem_big.cpp | 58 +++++++++++-- src/oem_big.h | 40 ++++++--- src/oem_dense.cpp | 54 +++++++++++- src/oem_dense.h | 40 ++++++--- src/oem_init.c | 1 src/oem_logistic_dense.cpp | 53 ++++++++++-- src/oem_logistic_dense.h | 40 ++++++--- src/oem_logistic_sparse.cpp | 52 ++++++++++-- src/oem_logistic_sparse.h | 40 ++++++--- src/oem_sparse.cpp | 52 ++++++++++-- src/oem_sparse.h | 40 ++++++--- src/oem_xtx.cpp | 54 ++++++++++-- src/oem_xtx.h | 40 ++++++--- src/oem_xval_dense.cpp | 53 ++++++++++-- src/oem_xval_dense.h | 40 ++++++--- vignettes/mult-1.png |binary vignettes/oem_vignette.Rmd | 6 - 43 files changed, 949 insertions(+), 446 deletions(-)
Title: Number Series Generator
Description: A number series generator that creates number series items based on cognitive models.
Author: Bao Sheng Loe (Aiden) [aut, cre, cph]
Maintainer: Bao Sheng Loe (Aiden) <bsl28@cam.ac.uk>
Diff between numGen versions 0.1.0 dated 2017-05-21 and 0.1.1 dated 2017-07-08
DESCRIPTION | 13 ++++++++----- MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 15 insertions(+), 7 deletions(-)
Title: Solve Systems of Nonlinear Equations
Description: Solve a system of nonlinear equations using a Broyden or a Newton method
with a choice of global strategies such as line search and trust region.
There are options for using a numerical or user supplied Jacobian,
for specifying a banded numerical Jacobian and for allowing
a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between nleqslv versions 3.3 dated 2017-05-18 and 3.3.1 dated 2017-07-08
DESCRIPTION | 8 +++---- MD5 | 12 +++++----- NEWS | 6 +++++ man/nleqslv.Rd | 2 - src/lautil.f | 47 ++++++++++++++++++++++++++++++++++++++++++ src/liqrev.f | 44 --------------------------------------- src/liqrup.f | 63 +++++++++++---------------------------------------------- 7 files changed, 77 insertions(+), 105 deletions(-)
Title: Multi-Objective Kriging Optimization
Description: Multi-Objective optimization based on the Kriging metamodel.
Important functions: mkm, VMPF, MEGO and HEGO.
Author: Adriano Passos [aut, cre],
Marco Luersen [ctb]
Maintainer: Adriano Passos <adriano.utfpr@gmail.com>
Diff between moko versions 1.0.0 dated 2016-09-16 and 1.0.1 dated 2017-07-08
moko-1.0.0/moko/R/visualise.R |only moko-1.0.0/moko/man/radviz.Rd |only moko-1.0.0/moko/tests |only moko-1.0.1/moko/DESCRIPTION | 10 moko-1.0.1/moko/MD5 | 74 ++-- moko-1.0.1/moko/NAMESPACE | 1 moko-1.0.1/moko/R/mkm.R | 492 +++++++++++++++--------------- moko-1.0.1/moko/R/moko.R | 2 moko-1.0.1/moko/R/optim_hego.R | 10 moko-1.0.1/moko/R/optim_mego.R | 18 - moko-1.0.1/moko/R/optim_vmpf.R | 4 moko-1.0.1/moko/R/ps.R | 2 moko-1.0.1/moko/R/ps_metrics.R | 8 moko-1.0.1/moko/R/test_functions.R | 8 moko-1.0.1/moko/R/utils.R | 62 +-- moko-1.0.1/moko/build/vignette.rds |binary moko-1.0.1/moko/inst/doc/nb_vignette.Rmd | 420 ++++++++++++------------- moko-1.0.1/moko/inst/doc/nb_vignette.html | 13 moko-1.0.1/moko/man/EHVI.Rd | 11 moko-1.0.1/moko/man/EI.Rd | 15 moko-1.0.1/moko/man/HEGO.Rd | 3 moko-1.0.1/moko/man/MEGO.Rd | 7 moko-1.0.1/moko/man/Tchebycheff.Rd | 5 moko-1.0.1/moko/man/VMPF.Rd | 5 moko-1.0.1/moko/man/igd.Rd | 7 moko-1.0.1/moko/man/max_EHVI.Rd | 3 moko-1.0.1/moko/man/max_EI.Rd | 7 moko-1.0.1/moko/man/mkm-class.Rd | 1 moko-1.0.1/moko/man/mkm.Rd | 1 moko-1.0.1/moko/man/moko.Rd | 3 moko-1.0.1/moko/man/nowacki_beam.Rd | 7 moko-1.0.1/moko/man/nowacki_beam_tps.Rd | 1 moko-1.0.1/moko/man/pdist.Rd | 3 moko-1.0.1/moko/man/predict-mkm-method.Rd | 3 moko-1.0.1/moko/man/predict_front.Rd | 5 moko-1.0.1/moko/man/ps.Rd | 3 moko-1.0.1/moko/man/test_functions.Rd | 9 moko-1.0.1/moko/vignettes/nb_vignette.Rmd | 420 ++++++++++++------------- moko-1.0.1/moko/vignettes/nb_vignette.bib | 15 39 files changed, 817 insertions(+), 841 deletions(-)
Title: Mathematical Morphology in Any Number of Dimensions
Description: Provides tools for performing mathematical morphology operations,
such as erosion and dilation, on data of arbitrary dimensionality. Can also
be used for finding connected components, resampling, filtering, smoothing
and other image processing-style operations.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between mmand versions 1.5.0 dated 2017-05-11 and 1.5.1 dated 2017-07-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 7 +++++++ src/Componenter.cpp | 17 +++++++++++++++-- src/Componenter.h | 2 ++ tests/testthat/test-25-components.R | 8 ++++++++ 6 files changed, 41 insertions(+), 11 deletions(-)
Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 0.5.5 dated 2017-01-19 and 0.5.6 dated 2017-07-08
MetaLandSim-0.5.5/MetaLandSim/R/spom.R |only MetaLandSim-0.5.6/MetaLandSim/DESCRIPTION | 15 - MetaLandSim-0.5.6/MetaLandSim/MD5 | 20 - MetaLandSim-0.5.6/MetaLandSim/NAMESPACE | 6 MetaLandSim-0.5.6/MetaLandSim/R/MetaLandSim.GUI.R | 9 MetaLandSim-0.5.6/MetaLandSim/R/metrics.graph.R | 205 ++++++++------ MetaLandSim-0.5.6/MetaLandSim/R/spom.r |only MetaLandSim-0.5.6/MetaLandSim/inst/doc/MetaLandSim.pdf |binary MetaLandSim-0.5.6/MetaLandSim/man/MetaLandSim-package.Rd | 5 MetaLandSim-0.5.6/MetaLandSim/man/manage_landscape_sim.Rd | 2 MetaLandSim-0.5.6/MetaLandSim/man/metrics.graph.Rd | 23 + MetaLandSim-0.5.6/MetaLandSim/man/span.graph.Rd | 10 12 files changed, 167 insertions(+), 128 deletions(-)
Title: The Moving Epidemic Method Web Application
Description: Web application created in the Shiny framework for the 'mem' R package.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between memapp versions 2.2 dated 2017-06-23 and 2.3 dated 2017-07-08
DESCRIPTION | 10 MD5 | 14 R/runmemapp.R | 2 README.md | 7 inst/shinyapp/helpers.R | 55 +- inst/shinyapp/server.R | 980 ++++++++++++++++++++++++++---------------------- inst/shinyapp/ui.R | 26 - man/runmemapp.Rd | 2 8 files changed, 616 insertions(+), 480 deletions(-)
Title: The Moving Epidemic Method R Package
Description: Tools to model influenza epidemics and to monitor influenza surveillance.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between mem versions 2.8 dated 2017-06-23 and 2.9 dated 2017-07-08
DESCRIPTION | 8 - MD5 | 92 ++++++++-------- NAMESPACE | 1 R/calcular.indicadores.2.timings.R | 16 ++ R/calcular.indicadores.R | 40 ++++--- R/epimem.R | 2 R/epitiming.R | 2 R/flucyl.R | 23 ++-- R/flucylraw.R | 2 R/full.series.graph.R | 66 ++++++----- R/mem-package.R | 63 +++++++++-- R/memevolution.R | 64 ++++++++--- R/memgoodness.R | 88 +++++++++++---- R/memintensity.R | 87 ++++++++------- R/memmodel.R | 167 ++++++++++++++++++++--------- R/memstability.R | 45 +++++--- R/memsurveillance.R | 52 ++++++--- R/memsurveillance.animated.R | 39 ++++-- R/memtiming.R | 104 ++++++++++-------- R/memtrend.R | 79 +++++++------- R/optimum.by.inspection.R | 207 +++++++++++++++++++++++++++---------- R/processPlots.R | 33 +++-- R/roc.analysis.R | 42 ++++--- R/transformdata.R | 34 +++--- R/transformdata.back.R | 35 +++--- R/transformseries.R | 62 ++++++----- man/epimem.Rd | 2 man/epitiming.Rd | 2 man/flucyl.Rd | 23 ++-- man/flucylraw.Rd | 2 man/full.series.graph.Rd | 60 ++++++---- man/mem-package.Rd | 63 +++++++++-- man/memevolution.Rd | 60 ++++++++-- man/memgoodness.Rd | 75 ++++++++++--- man/memintensity.Rd | 71 ++++++------ man/memmodel.Rd | 125 ++++++++++++++++------ man/memstability.Rd | 39 ++++-- man/memsurveillance.Rd | 38 +++++- man/memsurveillance.animated.Rd | 27 ++-- man/memtiming.Rd | 60 ++++++---- man/memtrend.Rd | 55 +++++---- man/optimum.by.inspection.Rd | 48 +++++--- man/processPlots.Rd | 27 ++-- man/roc.analysis.Rd | 38 ++++-- man/transformdata.Rd | 27 ++-- man/transformdata.back.Rd | 29 +++-- man/transformseries.Rd | 48 +++++--- 47 files changed, 1556 insertions(+), 816 deletions(-)
Title: Visualising Molecular Dynamics Analyses
Description: Provides automatization for plot generation succeeding common molecular dynamics analyses.
This includes straightforward plots, such as RMSD (Root-Mean-Square-Deviation) and
RMSF (Root-Mean-Square-Fluctuation) but also more sophisticated ones such as
dihedral angle maps, hydrogen bonds, cluster bar plots and
DSSP (Definition of Secondary Structure of Proteins) analysis. Currently able to load
GROMOS, GROMACS and AMBER formats, respectively.
Author: Christian Margreitter [aut, cre], Chris Oostenbrink [aut]
Maintainer: Christian Margreitter <christian.margreitter@gmail.com>
Diff between MDplot versions 1.0.0 dated 2017-02-23 and 1.0.1 dated 2017-07-08
DESCRIPTION | 18 +++-- MD5 | 41 ++++++----- NEWS | 9 ++ R/timeseries.R | 88 +++++++++++++++++++------ build |only inst/CITATION | 28 +++++-- inst/bash/MDplot_bash.R | 9 +- inst/doc |only inst/extdata/timeseries_example_GROMACS.txt.gz |only man/clusters.Rd | 2 man/clusters_ts.Rd | 2 man/dssp.Rd | 2 man/dssp_ts.Rd | 2 man/hbond.Rd | 2 man/hbond_ts.Rd | 11 +-- man/load_hbond_ts.Rd | 12 ++- man/load_ramchandran.Rd | 2 man/load_timeseries.Rd | 10 ++ man/ramachandran.Rd | 4 - man/rmsd.Rd | 2 man/rmsf.Rd | 2 man/timeseries.Rd | 9 ++ vignettes |only 23 files changed, 175 insertions(+), 80 deletions(-)
Title: Bayesian Non-Parametric Latent-Class Capture-Recapture
Description: Bayesian population size estimation using non parametric latent-class models.
Author: Daniel Manrique-Vallier
Maintainer: Daniel Manrique-Vallier <dmanriqu@indiana.edu>
Diff between LCMCR versions 0.4.1 dated 2016-02-11 and 0.4.3 dated 2017-07-08
DESCRIPTION | 10 +++++----- MD5 | 31 ++++++++++++++++--------------- NAMESPACE | 6 +----- man/LCMCR-package.Rd | 4 ++-- man/lcmCR.Rd | 4 ++-- src/Makevars | 2 +- src/Makevars.win | 2 +- src/NPLCM_CR_Basic_Freq.cpp | 14 ++++++++------ src/daniel2/CData.h | 6 +++--- src/daniel2/CParam.h | 2 +- src/daniel2/CParam_generic.cpp | 4 ++-- src/daniel2/CVariable_Container.cpp | 4 ++-- src/daniel2/R_Environ_Simple.cpp | 12 ++++++++---- src/daniel2/dan_array_utils.cpp | 4 ++-- src/daniel2/dan_array_utils.h | 8 ++++---- src/daniel2/dan_sys.h | 8 ++++---- src/registration.cpp |only 17 files changed, 62 insertions(+), 59 deletions(-)
Title: Categorical Landscape Simulation Facility
Description: Simulates categorical maps on actual geographical realms, starting from either empty landscapes or landscapes provided by the user (e.g. land use maps). Allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscapes in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion) and von Neumann neighbourhood (four cells, aka Rook case). Outputs are raster dataset exportable to any common GIS format.
Author: Dario Masante [aut, cre]
Maintainer: Dario Masante <dario.masante@gmail.com>
Diff between landscapeR versions 1.1.3 dated 2016-12-13 and 1.2 dated 2017-07-08
DESCRIPTION | 15 +++++---- MD5 | 44 +++++++++++++++------------- NAMESPACE | 2 + NEWS.md | 9 +++++ R/RcppExports.R |only R/expandClass.R | 23 ++++++++------- R/landscapeR-package.R | 5 ++- R/makeClass.R | 6 +-- R/makeLine.R | 44 ++++++++++++++++------------ R/makePatch.R | 70 +++++++++++++++------------------------------- R/zzz.R | 6 +++ build/vignette.rds |binary inst/doc/landscapeR.R | 10 +++--- inst/doc/landscapeR.Rmd | 15 +++++---- inst/doc/landscapeR.html | 45 +++++++++++++---------------- man/expandClass.Rd | 1 man/landscapeR-package.Rd | 6 +-- man/makeClass.Rd | 1 man/makeLine.Rd | 1 man/makePatch.Rd | 1 man/rmSingle.Rd | 1 src |only vignettes/landscapeR.Rmd | 15 +++++---- 23 files changed, 161 insertions(+), 159 deletions(-)
Title: Deconvolution for LINCS L1000 Data
Description: LINCS L1000 is a high-throughput technology that allows the gene expression measurement in a large number of assays. However, to fit the measurements of ~1000 genes in the ~500 color channels of LINCS L1000, every two landmark genes are designed to share a single channel. Thus, a deconvolution step is required to infer the expression values of each gene. Any errors in this step can be propagated adversely to the downstream analyses. We present a LINCS L1000 data peak calling R package l1kdeconv based on a new outlier detection method and an aggregate Gaussian mixture model. Upon the remove of outliers and the borrowing information among similar samples, l1kdeconv shows more stable and better performance than methods commonly used in LINCS L1000 data deconvolution.
Author: Zhao Li[aut], Peng Yu[aut, cre]
Maintainer: Zhao Li <lizhao.informatics@gmail.com>
Diff between l1kdeconv versions 1.1.0 dated 2017-04-17 and 1.2.0 dated 2017-07-08
DESCRIPTION | 12 ++++----- MD5 | 30 +++++++++++++++-------- NAMESPACE | 9 ++++++- R/getclusterranges.R | 2 - R/gmmplot.R |only R/multigmmmanydata.R |only R/multigmmplot.R |only R/multigmmsamedistribu.R | 49 +++++++++++++++++++++++++++------------ R/multigmmsamedistribulik.R | 2 - R/multigmmsamedistribumulti.R |only R/rmoutlier1d.R | 8 +++--- R/splitgrp.R |only man/getclusterranges.Rd | 4 +-- man/gmmplot.Rd |only man/multigmmmanydata.Rd |only man/multigmmplot.Rd |only man/multigmmsamedistribu.Rd | 21 +++++++++++----- man/multigmmsamedistribulik.Rd | 4 +-- man/multigmmsamedistribumulti.Rd |only man/rmoutlier1d.Rd | 8 +++--- man/splitgrp.Rd |only 21 files changed, 96 insertions(+), 53 deletions(-)
Title: A Quantified Implementation of the Kraljic Matrix
Description: Implements a quantified approach to the Kraljic Matrix (Kraljic, 1983, <https://hbr.org/1983/09/purchasing-must-become-supply-management>)
for strategically analyzing a firm’s purchasing portfolio. It combines multi-objective decision analysis to measure purchasing characteristics and
uses this information to place products and services within the Kraljic Matrix.
Author: Bradley Boehmke [aut, cre],
Robert Montgomery [ctb],
Ogden Jeffrey [ctb],
Jason Freels [ctb]
Maintainer: Bradley Boehmke <bradleyboehmke@gmail.com>
Diff between KraljicMatrix versions 0.1.1 dated 2017-02-21 and 0.1.2 dated 2017-07-08
DESCRIPTION | 14 +++++++------- MD5 | 25 +++++++++++++------------ build/vignette.rds |binary inst/doc/kraljic.html | 32 ++++++++++++++++---------------- man/MAVF_score.Rd | 1 - man/MAVF_sensitivity.Rd | 1 - man/SAVF_plot.Rd | 1 - man/SAVF_plot_rho_error.Rd | 1 - man/SAVF_preferred_rho.Rd | 1 - man/SAVF_score.Rd | 1 - man/kraljic_matrix.Rd | 1 - man/kraljic_quadrant.Rd | 1 - man/psc.Rd | 1 - tools |only 14 files changed, 36 insertions(+), 44 deletions(-)
Title: GUI for Cohen's and Fleiss' Kappa
Description: Offers a Shiny user interface to work out Cohen's and Fleiss' Kappa.
Author: Frederic Santos
Maintainer: Frederic Santos <frederic.santos@u-bordeaux.fr>
Diff between KappaGUI versions 1.2.1 dated 2017-06-22 and 2.0.0 dated 2017-07-08
KappaGUI-1.2.1/KappaGUI/R/Sel_procedure.R |only KappaGUI-1.2.1/KappaGUI/R/datafile_details.R |only KappaGUI-1.2.1/KappaGUI/man/Sel_procedure.Rd |only KappaGUI-1.2.1/KappaGUI/man/datafile_details.Rd |only KappaGUI-2.0.0/KappaGUI/DESCRIPTION | 12 +-- KappaGUI-2.0.0/KappaGUI/MD5 | 17 ++-- KappaGUI-2.0.0/KappaGUI/NAMESPACE | 4 - KappaGUI-2.0.0/KappaGUI/R/StartKappa.R | 86 ------------------------ KappaGUI-2.0.0/KappaGUI/inst |only KappaGUI-2.0.0/KappaGUI/man/KappaGUI-package.Rd | 14 +-- KappaGUI-2.0.0/KappaGUI/man/StartKappa.Rd | 19 ++--- 11 files changed, 34 insertions(+), 118 deletions(-)
Title: Individual Tree Crowns Segmentation
Description: Three methods for Individual Tree Crowns (ITCs) delineation on remote sensing data: one is based on LiDAR data in x,y,z format and one on imagery data in raster format.
Author: Michele Dalponte
Maintainer: Michele Dalponte <michele.dalponte@fmach.it>
Diff between itcSegment versions 0.5 dated 2017-05-23 and 0.6 dated 2017-07-08
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ R/agb.R | 2 +- R/dbh.R | 31 +++++++++++++++++++++++++++++-- R/itcLiDAR.R | 2 +- R/itcLiDARallo.R | 2 +- man/agb.Rd | 7 +++---- man/dbh.Rd | 7 +++---- man/imgData.Rd | 1 - man/itcIMG.Rd | 7 +++---- man/itcLiDAR.Rd | 7 +++---- man/itcLiDARallo.Rd | 7 +++---- man/lasData.Rd | 1 - 13 files changed, 64 insertions(+), 44 deletions(-)
Title: Isoscape Computation and Inference of Spatial Origins using
Mixed Models
Description:
Building isoscapes using mixed models and inferring the geographic origin of
organisms based on their isotopic ratios. This package is essentially a
simplified interface to several other packages. It uses 'spaMM' for fitting
and predicting isoscapes, and assigning an organism's origin depending on its
isotopic ratio. 'IsoriX' also relies heavily on the package 'rasterVis' for
plotting the maps using lattice.
Author:
Alexandre Courtiol [aut, cre],
François Rousset [aut],
Marie-Sophie Rohwaeder [aut],
Stephanie Kramer-Schadt [aut, cre]
Maintainer: Alexandre Courtiol <alexandre.courtiol@gmail.com>
Diff between IsoriX versions 0.5 dated 2017-04-12 and 0.6 dated 2017-07-08
IsoriX-0.5/IsoriX/R/IsoriX-internal.R |only IsoriX-0.5/IsoriX/R/isorix.R |only IsoriX-0.5/IsoriX/R/plot.calibfit.R |only IsoriX-0.5/IsoriX/R/plot.isofit.R |only IsoriX-0.5/IsoriX/R/plot.methods.R |only IsoriX-0.5/IsoriX/data/Europefit.rda |only IsoriX-0.5/IsoriX/data/GNIPdata.rda |only IsoriX-0.5/IsoriX/data/assigndata.rda |only IsoriX-0.5/IsoriX/data/calibdata.rda |only IsoriX-0.5/IsoriX/data/countries.rda |only IsoriX-0.5/IsoriX/data/elevraster.rda |only IsoriX-0.5/IsoriX/data/oceanmask.rda |only IsoriX-0.5/IsoriX/man/Europefit.Rd |only IsoriX-0.5/IsoriX/man/GNIPdata.Rd |only IsoriX-0.5/IsoriX/man/assigndata.Rd |only IsoriX-0.5/IsoriX/man/calibdata.Rd |only IsoriX-0.5/IsoriX/man/elevraster.Rd |only IsoriX-0.5/IsoriX/man/isopalettes.Rd |only IsoriX-0.5/IsoriX/man/isorix.Rd |only IsoriX-0.5/IsoriX/man/oceanmask.Rd |only IsoriX-0.5/IsoriX/man/plot.methods.Rd |only IsoriX-0.5/IsoriX/man/worldcountries.Rd |only IsoriX-0.6/IsoriX/DESCRIPTION | 24 IsoriX-0.6/IsoriX/MD5 | 120 +- IsoriX-0.6/IsoriX/NAMESPACE | 69 - IsoriX-0.6/IsoriX/R/IsoriX-dataset.R |only IsoriX-0.6/IsoriX/R/IsoriX-package.R |only IsoriX-0.6/IsoriX/R/calibfit.R | 326 ++++-- IsoriX-0.6/IsoriX/R/create_aliens.R |only IsoriX-0.6/IsoriX/R/getelev.R | 182 ++- IsoriX-0.6/IsoriX/R/internalfunctions.R |only IsoriX-0.6/IsoriX/R/isofind.R |only IsoriX-0.6/IsoriX/R/isofit.R | 742 ++++++++++----- IsoriX-0.6/IsoriX/R/isoscape.R | 585 ++++++++--- IsoriX-0.6/IsoriX/R/isosim.R | 449 +++++---- IsoriX-0.6/IsoriX/R/options.R |only IsoriX-0.6/IsoriX/R/plots.R |only IsoriX-0.6/IsoriX/R/prepcipitate.R |only IsoriX-0.6/IsoriX/R/queryGNIP.R | 354 +++++-- IsoriX-0.6/IsoriX/R/relevate.R | 215 +++- IsoriX-0.6/IsoriX/build/vignette.rds |binary IsoriX-0.6/IsoriX/data/AssignDataAlien.rda |only IsoriX-0.6/IsoriX/data/AssignDataBat.rda |only IsoriX-0.6/IsoriX/data/CalibDataAlien.rda |only IsoriX-0.6/IsoriX/data/CalibDataBat.rda |only IsoriX-0.6/IsoriX/data/CountryBorders.rda |only IsoriX-0.6/IsoriX/data/ElevRasterDE.rda |only IsoriX-0.6/IsoriX/data/GNIPDataDE.rda |only IsoriX-0.6/IsoriX/data/OceanMask.rda |only IsoriX-0.6/IsoriX/data/datalist | 16 IsoriX-0.6/IsoriX/inst/CITATION | 2 IsoriX-0.6/IsoriX/inst/NEWS.Rd | 101 +- IsoriX-0.6/IsoriX/inst/doc/IUCNmask.pdf |only IsoriX-0.6/IsoriX/inst/doc/IUCNmask.pdf.asis |only IsoriX-0.6/IsoriX/inst/doc/Precipitation.pdf |only IsoriX-0.6/IsoriX/inst/doc/Precipitation.pdf.asis |only IsoriX-0.6/IsoriX/inst/doc/Saveplot.pdf |binary IsoriX-0.6/IsoriX/inst/doc/Workflow.pdf |binary IsoriX-0.6/IsoriX/inst/doc/exportGIS.pdf |binary IsoriX-0.6/IsoriX/inst/doc/sources_for_IUCNmask.Rmd |only IsoriX-0.6/IsoriX/inst/doc/sources_for_Precipitation.Rmd |only IsoriX-0.6/IsoriX/inst/doc/sources_for_Saveplot.Rmd | 73 - IsoriX-0.6/IsoriX/inst/doc/sources_for_Workflow.Rmd | 400 ++++---- IsoriX-0.6/IsoriX/inst/doc/sources_for_exportGIS.Rmd | 78 - IsoriX-0.6/IsoriX/man/AssignDataAlien.Rd |only IsoriX-0.6/IsoriX/man/AssignDataBat.Rd |only IsoriX-0.6/IsoriX/man/CalibDataAlien.Rd |only IsoriX-0.6/IsoriX/man/CalibDataBat.Rd |only IsoriX-0.6/IsoriX/man/CountryBorders.Rd |only IsoriX-0.6/IsoriX/man/ElevRasterDE.Rd |only IsoriX-0.6/IsoriX/man/GNIPDataDE.Rd |only IsoriX-0.6/IsoriX/man/IsoriX-defunct.Rd | 39 IsoriX-0.6/IsoriX/man/IsoriX-package.Rd | 143 ++ IsoriX-0.6/IsoriX/man/OceanMask.Rd |only IsoriX-0.6/IsoriX/man/calibfit.Rd | 122 +- IsoriX-0.6/IsoriX/man/create_aliens.Rd |only IsoriX-0.6/IsoriX/man/getelev.Rd | 70 - IsoriX-0.6/IsoriX/man/getprecip.Rd |only IsoriX-0.6/IsoriX/man/isofind.Rd |only IsoriX-0.6/IsoriX/man/isofit.Rd | 300 +++--- IsoriX-0.6/IsoriX/man/isomultifit.Rd |only IsoriX-0.6/IsoriX/man/isomultiscape.Rd |only IsoriX-0.6/IsoriX/man/isopalette2.Rd |only IsoriX-0.6/IsoriX/man/isoscape.Rd | 220 +--- IsoriX-0.6/IsoriX/man/isosim.Rd | 230 ++-- IsoriX-0.6/IsoriX/man/options.Rd |only IsoriX-0.6/IsoriX/man/plots.Rd |only IsoriX-0.6/IsoriX/man/prepcipitate.Rd |only IsoriX-0.6/IsoriX/man/queryGNIP.Rd | 207 ++-- IsoriX-0.6/IsoriX/man/relevate.Rd | 234 ++-- IsoriX-0.6/IsoriX/vignettes/IUCNmask.pdf.asis |only IsoriX-0.6/IsoriX/vignettes/Precipitation.pdf.asis |only IsoriX-0.6/IsoriX/vignettes/Style_Guide.Rmd |only 93 files changed, 3455 insertions(+), 1846 deletions(-)
Title: Classes and Methods for Seismic Data Analysis
Description: Provides classes and methods for seismic data analysis. The
base classes and methods are inspired by the python code found in
the 'ObsPy' python toolbox <https://github.com/obsypy/obspy>. Additional classes and
methods support data returned by web services provided by the 'IRIS DMC'
<http://service.iris.edu/>.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Gillian Sharer [aut, cre],
Mary Templeton [aut],
Chad Trabant [ctb]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>
Diff between IRISSeismic versions 1.4.5 dated 2017-06-09 and 1.4.6 dated 2017-07-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/Class-Trace.R | 14 ++++++++------ man/IRISSeismic-package.Rd | 5 +++++ 4 files changed, 19 insertions(+), 12 deletions(-)
Title: Miscellaneous Functions for the USGS INL Project Office
Description: A collection of functions for creating high-level graphics,
performing raster-based analysis, processing MODFLOW-based models, and
overlaying multi-polygon objects. Used to support packages and scripts written
by researchers at the United States Geological Survey (USGS)
Idaho National Laboratory (INL) Project Office.
Author: Jason C. Fisher [aut, cre]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Diff between inlmisc versions 0.2.6 dated 2017-04-01 and 0.2.7 dated 2017-07-08
DESCRIPTION | 13 +-- MD5 | 94 ++++++++++++----------- NAMESPACE | 3 NEWS.md | 17 ++++ R/AddColorKey.R | 18 ++-- R/AddInsetMap.R | 14 +-- R/AddPoints.R | 48 +++++------ R/AddScaleBar.R | 15 +-- R/BumpDisconnectCells.R | 10 +- R/BumpRiverStage.R | 8 - R/CreateWebMap.R |only R/ExportRasterStack.R | 10 +- R/ExtractAlongTransect.R | 6 - R/FormatPval.R |only R/GetDaysInMonth.R | 4 R/POSIXct2Character.R | 12 +- R/PlotCrossSection.R | 36 ++++---- R/PlotGraph.R | 177 +++++++++++++++++++++++++++++--------------- R/PlotMap.R | 70 ++++++++--------- R/ReadCodeChunks.R | 6 - R/ReadModflowBinary.R | 10 +- R/RecreateLibrary.R |only R/ReplaceInTemplate.R | 4 R/RmSmallCellChunks.R | 4 R/SetPolygons.R | 10 +- R/SummariseBudget.R | 6 - R/ToScientific.R | 12 +- inst/misc/preamble.tex | 2 man/AddColorKey.Rd | 18 ++-- man/AddInsetMap.Rd | 14 +-- man/AddPoints.Rd | 48 +++++------ man/AddScaleBar.Rd | 15 +-- man/BumpDisconnectCells.Rd | 10 +- man/BumpRiverStage.Rd | 8 - man/CreateWebMap.Rd |only man/ExportRasterStack.Rd | 10 +- man/ExtractAlongTransect.Rd | 6 - man/FormatPval.Rd |only man/GetDaysInMonth.Rd | 4 man/POSIXct2Character.Rd | 12 +- man/PlotCrossSection.Rd | 56 ++++++------- man/PlotGraph.Rd | 98 +++++++++++++++--------- man/PlotMap.Rd | 70 ++++++++--------- man/ReadCodeChunks.Rd | 6 - man/ReadModflowBinary.Rd | 8 - man/RecreateLibrary.Rd |only man/ReplaceInTemplate.Rd | 4 man/RmSmallCellChunks.Rd | 4 man/SetPolygons.Rd | 10 +- man/SummariseBudget.Rd | 6 - man/ToScientific.Rd | 12 +- 51 files changed, 572 insertions(+), 456 deletions(-)
Title: Fitting, Diagnostics, and Plotting Functions for Infinite
Mixtures of Infinite Factor Analysers and Related Models
Description: Provides flexible Bayesian estimation of Infinite Mixtures of Infinite Factor Analysers and related models, for nonparametrically clustering high-dimensional data, introduced by Murphy et al. (2017) <arXiv:1701.07010>. The IMIFA model conducts Bayesian nonparametric model-based clustering with factor analytic covariance structures without recourse to model selection criteria to choose the number of clusters or cluster-specific latent factors, mostly via efficient Gibbs updates. Model-specific diagnostic tools are also provided, as well as many options for plotting results and conducting posterior inference on parameters of interest.
Author: Keefe Murphy [aut, cre],
Isobel Claire Gormley [ctb],
Cinzia Viroli [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>
Diff between IMIFA versions 1.3.0 dated 2017-06-21 and 1.3.1 dated 2017-07-08
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- NEWS.md | 5 +++ R/Diagnostics.R | 20 ++++++------ R/IMIFA.R | 6 +-- R/MainFunction.R | 16 ++++----- R/PlottingFunctions.R | 12 +++---- inst/doc/IMIFA.html | 8 ++-- man/IMIFA.Rd | 4 +- vignettes/res_olive_IMIFA__Edited-Vignette-only-Version.rda |binary 10 files changed, 51 insertions(+), 46 deletions(-)
Title: IMAGing engINE, Tools for Application of Image Filters to Data
Matrices
Description: Provides fast application of image filters to data matrices,
using R and C++ algorithms.
Author: Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between imagine versions 1.2.2 dated 2017-06-27 and 1.3.1 dated 2017-07-08
DESCRIPTION | 8 +- MD5 | 18 +++--- R/RcppExports.R | 4 - R/imagine-internal.R | 7 ++ R/imagine-main.R | 8 +- build/vignette.rds |binary inst/doc/vignette.html | 8 +- man/convolutions.Rd | 5 + src/RcppExports.cpp | 9 +-- src/engines.cpp | 145 ++++++++++++++++++++++++++++++------------------- 10 files changed, 130 insertions(+), 82 deletions(-)
Title: Intrinsic Dimension for Data Mining
Description: Contains techniques for mining large high-dimensional data sets
by using the concept of Intrinsic Dimension (ID). Here the ID is
not necessarily integer. It is extended to fractal dimensions. And
the Morisita estimator is used for the ID estimation, but other
tools are included as well.
Author: Jean Golay and Mohamed Laib
Maintainer: Jean Golay <Jean.Golay@unil.ch>
Diff between IDmining versions 1.0.1 dated 2017-06-15 and 1.0.2 dated 2017-07-08
DESCRIPTION | 19 +++++++++---------- MD5 | 41 +++++++++++++++++++++++++---------------- NAMESPACE | 9 +++++++++ R/Butterfly.R | 13 +++++-------- R/IDmining.R | 2 +- R/MBFR.r |only R/MBFR_parallel.R |only R/MBRM.R |only R/MBRM_parallel.R |only R/MINDEX_SP.R | 7 +++---- R/MINDID.R | 24 +++++++++++------------- R/MINDID_SFS.R |only R/RenDim.R | 24 +++++++++++------------- R/SwissRoll.R | 3 +-- R/logMINDEX.R | 21 ++++++++++----------- man/Butterfly.Rd | 3 +-- man/IDmining-package.Rd | 2 +- man/MBFR.Rd |only man/MBFR_parallel.Rd |only man/MBRM.Rd |only man/MBRM_parallel.Rd |only man/MINDEX_SP.Rd | 7 +++---- man/MINDID.Rd | 24 +++++++++++------------- man/RenDim.Rd | 24 +++++++++++------------- man/SwissRoll.Rd | 3 +-- man/logMINDEX.Rd | 21 ++++++++++----------- 26 files changed, 123 insertions(+), 124 deletions(-)
Title: The Hyperdirichlet Distribution, Mark 2
Description: A suite of routines for the hyperdirichlet distribution; supersedes the hyperdirichlet package for most purposes.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between hyper2 versions 1.0 dated 2017-06-28 and 1.0-1 dated 2017-07-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/hyper2.R | 2 +- inst/doc/hyper2.pdf |binary inst/rowing_minimal.txt | 33 ++++++++++++--------------------- src/hyperdirichlet2.cpp | 2 +- 6 files changed, 22 insertions(+), 31 deletions(-)
Title: Statistical Object Oriented Data Analysis of RDP-Based Taxonomic
Trees from Human Microbiome Data
Description: Tools to model, compare, and visualize populations of taxonomic tree objects.
Author: Patricio S. La Rosa, Elena Deych, Berkley Shands, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between HMPTrees versions 1.3 dated 2016-01-19 and 1.4 dated 2017-07-08
HMPTrees-1.3/HMPTrees/man/transformHMPTreetoHMP.Rd |only HMPTrees-1.3/HMPTrees/man/transformHMPtoHMPTree.Rd |only HMPTrees-1.4/HMPTrees/DESCRIPTION | 11 HMPTrees-1.4/HMPTrees/MD5 | 90 ++---- HMPTrees-1.4/HMPTrees/NAMESPACE | 5 HMPTrees-1.4/HMPTrees/NEWS | 83 +++-- HMPTrees-1.4/HMPTrees/R/buildTree.R | 58 ++- HMPTrees-1.4/HMPTrees/R/checkTreeValidHelp.R | 54 ++- HMPTrees-1.4/HMPTrees/R/checkTreeValidity.R | 47 +-- HMPTrees-1.4/HMPTrees/R/compareTwoDataSets.R | 139 +++++---- HMPTrees-1.4/HMPTrees/R/createAndPlot.R | 34 +- HMPTrees-1.4/HMPTrees/R/createTrees.R | 53 +-- HMPTrees-1.4/HMPTrees/R/displayLegend.R | 40 +- HMPTrees-1.4/HMPTrees/R/formatData.R | 37 +- HMPTrees-1.4/HMPTrees/R/generateTree.R | 53 +-- HMPTrees-1.4/HMPTrees/R/getBranchSizes.R | 84 ++--- HMPTrees-1.4/HMPTrees/R/getMLEandLoglike.R | 147 +++++----- HMPTrees-1.4/HMPTrees/R/getTaxaDepth.R | 54 +-- HMPTrees-1.4/HMPTrees/R/mergeDataSets.R | 90 +++--- HMPTrees-1.4/HMPTrees/R/pairedCompareTwoDataSets.R | 108 ++++--- HMPTrees-1.4/HMPTrees/R/plotTree.R | 68 ++-- HMPTrees-1.4/HMPTrees/R/plotTreeDataMDS.R | 145 ++++----- HMPTrees-1.4/HMPTrees/R/removeUnclass.R | 32 +- HMPTrees-1.4/HMPTrees/R/subsetData.R | 22 - HMPTrees-1.4/HMPTrees/R/transformHMPTreetoHMP.R | 29 - HMPTrees-1.4/HMPTrees/R/transformHMPtoHMPTree.R | 12 HMPTrees-1.4/HMPTrees/R/traverseTree.R | 57 +-- HMPTrees-1.4/HMPTrees/R/traverseTreeHelp.R | 109 +++---- HMPTrees-1.4/HMPTrees/R/trimToTaxaLevel.R | 46 +-- HMPTrees-1.4/HMPTrees/build/vignette.rds |binary HMPTrees-1.4/HMPTrees/inst/doc/Creating-Data-From-RDP-Tutorial.Rnw | 6 HMPTrees-1.4/HMPTrees/inst/doc/Creating-Data-From-RDP-Tutorial.pdf |binary HMPTrees-1.4/HMPTrees/man/HMPTrees-internal.Rd | 3 HMPTrees-1.4/HMPTrees/man/checkTreeValidity.Rd | 6 HMPTrees-1.4/HMPTrees/man/compareTwoDataSets.Rd | 32 +- HMPTrees-1.4/HMPTrees/man/createAndPlot.Rd | 16 - HMPTrees-1.4/HMPTrees/man/createTrees.Rd | 10 HMPTrees-1.4/HMPTrees/man/displayLegend.Rd | 4 HMPTrees-1.4/HMPTrees/man/formatData.Rd | 4 HMPTrees-1.4/HMPTrees/man/generateTree.Rd | 19 - HMPTrees-1.4/HMPTrees/man/getMLEandLoglike.Rd | 11 HMPTrees-1.4/HMPTrees/man/mergeDataSets.Rd | 7 HMPTrees-1.4/HMPTrees/man/pairedCompareTwoDataSets.Rd | 24 - HMPTrees-1.4/HMPTrees/man/plotTree.Rd | 15 - HMPTrees-1.4/HMPTrees/man/plotTreeDataMDS.Rd | 26 - HMPTrees-1.4/HMPTrees/man/trimToTaxaLevel.Rd | 2 HMPTrees-1.4/HMPTrees/vignettes/Creating-Data-From-RDP-Tutorial.Rnw | 6 47 files changed, 1005 insertions(+), 893 deletions(-)
Title: Hypothesis Testing and Power Calculations for Comparing
Metagenomic Samples from HMP
Description: Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.
Author: Patricio S. La Rosa, Elena Deych, Sharina Carter, Berkley Shands, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between HMP versions 1.4.3 dated 2016-03-04 and 1.5 dated 2017-07-08
HMP-1.4.3/HMP/R/LLDM.R |only HMP-1.4.3/HMP/R/Xoc.statistics.MoM.R |only HMP-1.4.3/HMP/man/kullbackLeiber.Rd |only HMP-1.4.3/HMP/man/pioest.Rd |only HMP-1.5/HMP/DESCRIPTION | 13 +- HMP-1.5/HMP/MD5 | 153 +++++++++++++++------------ HMP-1.5/HMP/NAMESPACE | 12 +- HMP-1.5/HMP/NEWS | 164 +++++++++++++++++------------ HMP-1.5/HMP/R/Barchart.data.R | 14 +- HMP-1.5/HMP/R/C.alpha.multinomial.R | 34 +++--- HMP-1.5/HMP/R/DM.MoM.R | 29 +++-- HMP-1.5/HMP/R/DM.Rpart.Perm.R |only HMP-1.5/HMP/R/DM.Rpart.R |only HMP-1.5/HMP/R/Data.filter.R | 96 +++++++++++----- HMP-1.5/HMP/R/Dirichlet.multinomial.R | 31 ++--- HMP-1.5/HMP/R/Est.PI.R |only HMP-1.5/HMP/R/Gen.Alg.Consensus.R |only HMP-1.5/HMP/R/Gen.Alg.R |only HMP-1.5/HMP/R/Kullback.Leibler.R |only HMP-1.5/HMP/R/MC.Xdc.statistics.R | 68 +++++++----- HMP-1.5/HMP/R/MC.Xmc.statistics.R | 81 ++++++++------ HMP-1.5/HMP/R/MC.Xmcupo.statistics.R | 87 ++++++++------- HMP-1.5/HMP/R/MC.Xoc.statistics.R | 52 +++++---- HMP-1.5/HMP/R/MC.Xsc.statistics.R | 48 +++++--- HMP-1.5/HMP/R/MC.ZT.statistics.R | 54 +++++---- HMP-1.5/HMP/R/Multinomial.R | 29 ++--- HMP-1.5/HMP/R/Plot.MDS.R |only HMP-1.5/HMP/R/Plot.PI.R |only HMP-1.5/HMP/R/T.statistics.R | 12 +- HMP-1.5/HMP/R/Test.Paired.R |only HMP-1.5/HMP/R/Xdc.sevsample.R | 47 ++++---- HMP-1.5/HMP/R/Xdc.statistics.Hnull.Ha.R | 43 +++---- HMP-1.5/HMP/R/Xdc.statistics.MoM.R | 25 ++-- HMP-1.5/HMP/R/Xdc.statistics.R | 31 ++--- HMP-1.5/HMP/R/Xmc.sevsample.R | 56 +++++---- HMP-1.5/HMP/R/Xmc.statistics.Hnull.Ha.R | 42 +++---- HMP-1.5/HMP/R/Xmc.statistics.R | 33 ++--- HMP-1.5/HMP/R/Xmcupo.effectsize.R | 86 +++++++++------ HMP-1.5/HMP/R/Xmcupo.sevsample.R | 53 +++++---- HMP-1.5/HMP/R/Xmcupo.statistics.Hnull.Ha.R | 60 +++++----- HMP-1.5/HMP/R/Xmcupo.statistics.R | 43 ++++--- HMP-1.5/HMP/R/Xoc.sevsample.R | 32 +++-- HMP-1.5/HMP/R/Xoc.statistics.Hnull.Ha.R | 33 +++-- HMP-1.5/HMP/R/Xoc.statistics.R | 34 +++--- HMP-1.5/HMP/R/Xsc.onesample.R | 37 +++--- HMP-1.5/HMP/R/Xsc.statistics.Hnull.Ha.R | 24 ++-- HMP-1.5/HMP/R/Xsc.statistics.R | 15 +- HMP-1.5/HMP/R/Z.statistics.R | 28 ++-- HMP-1.5/HMP/R/ZT.statistics.Hnull.Ha.R | 20 +-- HMP-1.5/HMP/R/calcRpartPval.R |only HMP-1.5/HMP/R/formatDataSets.R | 79 ++++++++----- HMP-1.5/HMP/R/gaCreation.R |only HMP-1.5/HMP/R/gaPlot.R |only HMP-1.5/HMP/R/gaScoring.R |only HMP-1.5/HMP/R/getBC.R |only HMP-1.5/HMP/R/kullbackLeiber.R | 48 -------- HMP-1.5/HMP/R/loglikDM.R | 16 +- HMP-1.5/HMP/R/pioest.R | 67 ++++++----- HMP-1.5/HMP/R/plotRpartPerm.R |only HMP-1.5/HMP/R/pruneRpart.R |only HMP-1.5/HMP/R/rpartEval.R |only HMP-1.5/HMP/R/rpartInit.R |only HMP-1.5/HMP/R/rpartSplit.R |only HMP-1.5/HMP/R/weirMoM.R | 34 +++--- HMP-1.5/HMP/data/hmp.pkg.env.rda |only HMP-1.5/HMP/man/C.alpha.multinomial.Rd | 4 HMP-1.5/HMP/man/DM.MoM.Rd | 4 HMP-1.5/HMP/man/DM.Rpart.Perm.Rd |only HMP-1.5/HMP/man/DM.Rpart.Rd |only HMP-1.5/HMP/man/Data.filter.Rd | 39 ++++-- HMP-1.5/HMP/man/Dirichlet.multinomial.Rd | 13 +- HMP-1.5/HMP/man/Est.Pi.Rd |only HMP-1.5/HMP/man/Gen.Alg.Consensus.Rd |only HMP-1.5/HMP/man/Gen.Alg.Rd |only HMP-1.5/HMP/man/HMP-internal.Rd | 16 ++ HMP-1.5/HMP/man/HMP-package.Rd | 10 - HMP-1.5/HMP/man/Kullback.Leibler.Rd |only HMP-1.5/HMP/man/MC.Xdc.statistics.Rd | 37 +++--- HMP-1.5/HMP/man/MC.Xmc.statistics.Rd | 43 ++++--- HMP-1.5/HMP/man/MC.Xmcupo.statistics.Rd | 36 +++--- HMP-1.5/HMP/man/MC.Xoc.statistics.Rd | 39 ++++-- HMP-1.5/HMP/man/MC.Xsc.statistics.Rd | 22 ++- HMP-1.5/HMP/man/MC.ZT.statistics.Rd | 24 ++-- HMP-1.5/HMP/man/Multinomial.Rd | 14 +- HMP-1.5/HMP/man/Plot.MDS.Rd |only HMP-1.5/HMP/man/Plot.Pi.Rd |only HMP-1.5/HMP/man/Test.Paired.Rd |only HMP-1.5/HMP/man/Xdc.sevsample.Rd | 8 - HMP-1.5/HMP/man/Xmc.sevsample.Rd | 12 +- HMP-1.5/HMP/man/Xmcupo.effectsize.Rd | 5 HMP-1.5/HMP/man/Xmcupo.sevsample.Rd | 7 - HMP-1.5/HMP/man/Xoc.sevsample.Rd | 9 + HMP-1.5/HMP/man/Xsc.onesample.Rd | 8 - HMP-1.5/HMP/man/formatDataSets.Rd | 14 +- 94 files changed, 1313 insertions(+), 1014 deletions(-)
Title: Graph-Based Change-Point Detection (g-Segmentation)
Description: Using an approach based on similarity graph to estimate change-point(s) and the corresponding p-values. Can be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure is available.
Author: Hao Chen, Nancy R. Zhang, and Lynna Chu
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Diff between gSeg versions 0.3 dated 2016-03-19 and 0.4 dated 2017-07-08
gSeg-0.3/gSeg/man/E.Rd |only gSeg-0.4/gSeg/DESCRIPTION | 11 gSeg-0.4/gSeg/MD5 | 22 gSeg-0.4/gSeg/NAMESPACE | 2 gSeg-0.4/gSeg/R/gSeg.r | 1142 ++++++++++++++++++++++++++++++++------ gSeg-0.4/gSeg/data/Example.rda |binary gSeg-0.4/gSeg/man/E1.Rd |only gSeg-0.4/gSeg/man/E2.Rd |only gSeg-0.4/gSeg/man/E3.Rd |only gSeg-0.4/gSeg/man/E4.Rd |only gSeg-0.4/gSeg/man/E5.Rd |only gSeg-0.4/gSeg/man/gSeg-package.Rd | 110 +++ gSeg-0.4/gSeg/man/gseg1.Rd | 79 ++ gSeg-0.4/gSeg/man/gseg2.Rd | 50 + gSeg-0.4/gSeg/man/n.Rd | 2 15 files changed, 1209 insertions(+), 209 deletions(-)
Title: Regularization Paths for Regression Models with Grouped
Covariates
Description: Efficient algorithms for fitting the regularization path of
linear or logistic regression models with grouped penalties. This
includes group selection methods such as group lasso, group MCP, and
group SCAD as well as bi-level selection methods such as the group
exponential lasso, the composite MCP, and the group bridge.
Author: Patrick Breheny [aut, cre], Yaohui Zeng [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between grpreg versions 3.1-1 dated 2017-06-08 and 3.1-2 dated 2017-07-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 5 +++++ inst/doc/penalties.pdf |binary inst/doc/quick-start.pdf |binary inst/tests/basic-functionality.R | 12 ++++++------ inst/tests/extra-features.R | 20 ++++++++++++++++++++ src/gdfit_gaussian.c | 3 +-- 8 files changed, 43 insertions(+), 19 deletions(-)
Title: Khmaladze Martingale Transformation Goodness-of-Fit Test
Description: Consider a goodness-of-fit(GOF) problem of testing whether a random sample comes from one sample location-scale model where location and scale parameters are unknown. It is well known that Khmaladze martingale transformation method provides asymptotic distribution free test for the GOF problem. This package contains one function: KhmaladzeTrans(). In this version, KhmaladzeTrans() provides test statistic and critical value of GOF test for normal, Cauchy, logistic, Gamma, Weibull, Gumbel, and Rayleigh distributions.
Author: Jiwoong Kim [aut, cre]
Maintainer: Jiwoong Kim <jwboys26@gmail.com>
Diff between GofKmt versions 1.0 dated 2016-04-19 and 2.0 dated 2017-07-08
GofKmt-1.0/GofKmt/R/KmtFunc.R |only GofKmt-2.0/GofKmt/DESCRIPTION | 8 ++++---- GofKmt-2.0/GofKmt/MD5 | 8 ++++---- GofKmt-2.0/GofKmt/NAMESPACE | 3 +-- GofKmt-2.0/GofKmt/R/RFuncLib-2D.R |only GofKmt-2.0/GofKmt/man/KhmaladzeTrans.Rd | 17 +++++++++++------ 6 files changed, 20 insertions(+), 16 deletions(-)
Title: Learning Interactions via Hierarchical Group-Lasso
Regularization
Description: Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper "Learning interactions via hierarchical group-lasso regularization" (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie (2015) <DOI:10.1080/10618600.2014.938812>.
Author: Michael Lim, Trevor Hastie
Maintainer: Michael Lim <michael626@gmail.com>
Diff between glinternet versions 1.0.4 dated 2017-06-15 and 1.0.5 dated 2017-07-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/glinternet.r | 5 +++++ 3 files changed, 11 insertions(+), 6 deletions(-)
Title: Tests for General Factorial Designs
Description: Implemented are the Wald-type statistic,
a permuted version thereof as well as the ANOVA-type statistic
for general factorial designs, even with non-normal error terms
and/or heteroscedastic variances, for crossed designs with an
arbitrary number of factors and nested designs with up to three factors.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@uni-ulm.de>
Diff between GFD versions 0.2.2 dated 2016-04-28 and 0.2.3 dated 2017-07-08
DESCRIPTION | 8 - MD5 | 20 ++-- R/GFD-function.R | 106 +++++++++++----------- R/hypo_matrix.R | 8 - R/plot_function.R | 192 ++++++++++++++++++++-------------------- build/vignette.rds |binary inst/doc/IntroductionToGFD.R | 4 inst/doc/IntroductionToGFD.Rmd | 16 ++- inst/doc/IntroductionToGFD.html | 36 ++++--- man/GFD.Rd | 9 + vignettes/IntroductionToGFD.Rmd | 16 ++- 11 files changed, 229 insertions(+), 186 deletions(-)
Title: Use and Explore CRU CL v. 2.0 Climatology Elements in R
Description: Provides functions that automate downloading and importing
University of East Anglia Climate Research Unit (CRU) CL v. 2.0 climatology
data into R, facilitates the calculation of minimum temperature and maximum
temperature and formats the data into a tidy data frame as a tibble or a
list of raster stack objects for use in an R session. CRU CL v. 2.0 data
are a gridded climatology of 1961-1990 monthly means released in 2002 and
cover all land areas (excluding Antarctica) at 10 arcminutes
(0.1666667 degree) resolution. For more information see the description of
the data provided by the University of East Anglia Climate Research Unit,
<https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.
Author: Adam Sparks [aut, cre] (http://orcid.org/0000-0002-0061-8359)
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between getCRUCLdata versions 0.1.7 dated 2017-06-26 and 0.1.8 dated 2017-07-08
DESCRIPTION | 8 MD5 | 42 - NEWS.md | 56 ++ R/create_CRU_df.R | 11 R/create_CRU_stack.R | 10 R/create_df.R | 2 R/get_CRU.R | 2 R/get_CRU_df.R | 2 R/get_CRU_stack.R | 2 R/set_cache.R | 6 README.md | 6 build/vignette.rds |binary inst/doc/getCRUCLdata.R | 6 inst/doc/getCRUCLdata.Rmd | 180 +++++-- inst/doc/getCRUCLdata.html | 155 ++++-- tests/testthat/test-create_CRU_df.R | 6 tests/testthat/test-create_CRU_stack.R | 744 ++++++++++++++++++++++++++++++++ tests/testthat/test-create_df.R | 753 ++++++++++++++++++++++++++++++++- tests/testthat/test-get_CRU_df.R | 16 tests/testthat/test-get_CRU_stack.R | 11 tests/testthat/test_set_cache.R | 4 vignettes/getCRUCLdata.Rmd | 180 +++++-- 22 files changed, 1987 insertions(+), 215 deletions(-)
Title: Furniture for Quantitative Scientists
Description: Contains two main functions (i.e., two pieces of furniture):
table1() which produces a well-formatted table of descriptives common as Table 1
in research articles and washer() which is helpful in cleaning up the data. In addition,
long() and wide(), built on the stats::reshape(), can help reformat the data.
These furniture functions are designed to simplify common tasks in
quantitative analysis. Other data summary and cleaning tools are also available.
Author: Tyson Barrett [aut, cre],
Emily Brignone [aut]
Maintainer: Tyson Barrett <t.barrett@aggiemail.usu.edu>
Diff between furniture versions 1.5.0 dated 2017-03-17 and 1.5.4 dated 2017-07-08
DESCRIPTION | 15 ++++++------ MD5 | 32 +++++++++++++++------------ NAMESPACE | 11 +++++++++ NEWS.md | 9 +++++++ R/Table1.R | 22 +++++++++++------- R/long_wide.R |only R/zzz.R | 2 - build/vignette.rds |binary inst/doc/Furniture.html | 48 ++++++++++++++++++++--------------------- inst/doc/Table1.Rmd | 2 - inst/doc/Table1.html | 8 +++--- man/long.Rd |only man/table1.Rd | 4 +-- man/table1_.Rd | 2 - man/wide.Rd |only tests/testthat/test_table1.R | 15 ++++++++++++ tests/testthat/test_widelong.R |only tests/testthat/test_xt.R | 2 - vignettes/Table1.Rmd | 2 - 19 files changed, 109 insertions(+), 65 deletions(-)
Title: Daily Streamflow Trend and Change Point Screening
Description: Screens daily streamflow time series for temporal trends and
change-points. This package has been primarily developed for assessing the
quality of daily streamflow time series. It also contains tools for plotting
and calculating many different streamflow metrics. The package can be used to
produce summary screening plots showing change-points and significant temporal
trends for high flow, low flow, and/or baseflow statistics, or it can be used
to perform more detailed hydrological time series analyses. The package was
designed for screening daily streamflow time series from Water Survey Canada
and the United States Geological Survey but will also work with streamflow time
series from many other agencies.
Author: Jennifer Dierauer [aut, cre],
Paul Whitfield [aut]
Maintainer: Jennifer Dierauer <jen.r.brand@gmail.com>
Diff between FlowScreen versions 1.2.2 dated 2017-06-14 and 1.2.3 dated 2017-07-08
DESCRIPTION | 30 +++++++------- MD5 | 86 ++++++++++++++++++++--------------------- R/MAMn.R | 2 man/FDC.Rd | 7 +-- man/FlowScreen.Rd | 4 - man/MAMn.Rd | 7 +-- man/NA.runs.Rd | 7 +-- man/NA.sum.Rd | 7 +-- man/Qn.Rd | 1 man/YMD.internal.Rd | 1 man/axis_doy.internal.Rd | 1 man/bf.seas.Rd | 7 +-- man/bf.stats.Rd | 1 man/bf_boughton.Rd | 7 +-- man/bf_eckhardt.Rd | 7 +-- man/bf_oneparam.Rd | 7 +-- man/cania.sub.ts.Rd | 1 man/caniapiscau.Rd | 1 man/caniapiscau.res.Rd | 1 man/create.ts.Rd | 1 man/dr.events.Rd | 7 +-- man/dr.pds.Rd | 7 +-- man/dr.seas.Rd | 7 +-- man/get.station.internal.Rd | 1 man/get.titles.internal.Rd | 1 man/hyear.internal.Rd | 1 man/metrics.all.Rd | 7 +-- man/mqt.Rd | 7 +-- man/pk.bf.stats.Rd | 1 man/pk.cov.Rd | 1 man/pk.max.Rd | 7 +-- man/pk.max.doy.Rd | 7 +-- man/pks.Rd | 1 man/pks.dur.Rd | 1 man/read.flows.Rd | 1 man/regime.Rd | 1 man/screen.cpts.Rd | 7 +-- man/screen.frames.Rd | 1 man/screen.frames.internal.Rd | 1 man/screen.metric.Rd | 7 +-- man/screen.series.Rd | 1 man/screen.summary.Rd | 7 +-- man/screen.summary.internal.Rd | 1 man/station.info.Rd | 1 44 files changed, 155 insertions(+), 115 deletions(-)
Title: Handy String and File Manipulation
Description: Convenient functions for moving files, deleting directories,
and a variety of string operations that facilitate manipulating file names
and extracting information from strings.
Author: Rory Nolan [aut, cre, cph],
Jim Hester [ctb],
Kirill Muller [ctb],
Sergi Padilla-Parra [ths]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between filesstrings versions 1.0.0 dated 2017-06-05 and 1.1.0 dated 2017-07-08
filesstrings-1.0.0/filesstrings/man/AllEqual.Rd |only filesstrings-1.0.0/filesstrings/man/BeforeLastDot.Rd |only filesstrings-1.0.0/filesstrings/man/CanBeNumeric.Rd |only filesstrings-1.0.0/filesstrings/man/CharListElemsNthElem.Rd |only filesstrings-1.0.0/filesstrings/man/CountMatches.Rd |only filesstrings-1.0.0/filesstrings/man/CreateDirsIfNotThere.Rd |only filesstrings-1.0.0/filesstrings/man/DuplicatesToSingles.Rd |only filesstrings-1.0.0/filesstrings/man/ExtendCharVec.Rd |only filesstrings-1.0.0/filesstrings/man/ExtractNumbers.Rd |only filesstrings-1.0.0/filesstrings/man/GetCurrencies.Rd |only filesstrings-1.0.0/filesstrings/man/GiveExt.Rd |only filesstrings-1.0.0/filesstrings/man/GroupClose.Rd |only filesstrings-1.0.0/filesstrings/man/LocateBraces.Rd |only filesstrings-1.0.0/filesstrings/man/MergeTablesOnDisk.Rd |only filesstrings-1.0.0/filesstrings/man/MoveFiles.Rd |only filesstrings-1.0.0/filesstrings/man/NiceFileNums.Rd |only filesstrings-1.0.0/filesstrings/man/NiceNums.Rd |only filesstrings-1.0.0/filesstrings/man/PasteCollapseListElems.Rd |only filesstrings-1.0.0/filesstrings/man/PasteDifferentLengths.Rd |only filesstrings-1.0.0/filesstrings/man/PutInPos.Rd |only filesstrings-1.0.0/filesstrings/man/RemoveDirs.Rd |only filesstrings-1.0.0/filesstrings/man/RemoveFileNameSpaces.Rd |only filesstrings-1.0.0/filesstrings/man/RemoveQuoted.Rd |only filesstrings-1.0.0/filesstrings/man/RenameWithNums.Rd |only filesstrings-1.0.0/filesstrings/man/SplitCamelCase.Rd |only filesstrings-1.0.0/filesstrings/man/StrAfterNth.Rd |only filesstrings-1.0.0/filesstrings/man/StrElem.Rd |only filesstrings-1.0.0/filesstrings/man/StrElemsPasted.Rd |only filesstrings-1.0.0/filesstrings/man/StrListRemoveEmpties.Rd |only filesstrings-1.0.0/filesstrings/man/StrSplitByNums.Rd |only filesstrings-1.0.0/filesstrings/man/StringToVec.Rd |only filesstrings-1.0.0/filesstrings/man/StringsWithPatterns.Rd |only filesstrings-1.0.0/filesstrings/man/TrimAnything.Rd |only filesstrings-1.0.0/filesstrings/man/UnitDirs.Rd |only filesstrings-1.0.0/filesstrings/src/init.c |only filesstrings-1.0.0/filesstrings/src/strings.cc |only filesstrings-1.1.0/filesstrings/DESCRIPTION | 6 filesstrings-1.1.0/filesstrings/MD5 | 120 +- filesstrings-1.1.0/filesstrings/NAMESPACE | 41 filesstrings-1.1.0/filesstrings/NEWS.md | 6 filesstrings-1.1.0/filesstrings/R/RcppExports.R | 46 - filesstrings-1.1.0/filesstrings/R/RcppExports_deprecated.R |only filesstrings-1.1.0/filesstrings/R/files.R | 105 +- filesstrings-1.1.0/filesstrings/R/files_deprecated.R |only filesstrings-1.1.0/filesstrings/R/filesstrings.R | 20 filesstrings-1.1.0/filesstrings/R/strings.R | 435 +++++----- filesstrings-1.1.0/filesstrings/R/strings_deprecated.R |only filesstrings-1.1.0/filesstrings/R/utils.R | 58 - filesstrings-1.1.0/filesstrings/R/utils_deprecated.R |only filesstrings-1.1.0/filesstrings/README.md | 16 filesstrings-1.1.0/filesstrings/inst/CITATION | 2 filesstrings-1.1.0/filesstrings/inst/doc/files.R | 22 filesstrings-1.1.0/filesstrings/inst/doc/files.Rmd | 28 filesstrings-1.1.0/filesstrings/inst/doc/files.html | 26 filesstrings-1.1.0/filesstrings/inst/doc/strings.R | 50 - filesstrings-1.1.0/filesstrings/inst/doc/strings.Rmd | 52 - filesstrings-1.1.0/filesstrings/inst/doc/strings.html | 58 - filesstrings-1.1.0/filesstrings/man/all_equal.Rd |only filesstrings-1.1.0/filesstrings/man/before_last_dot.Rd |only filesstrings-1.1.0/filesstrings/man/can_be_numeric.Rd |only filesstrings-1.1.0/filesstrings/man/count_matches.Rd |only filesstrings-1.1.0/filesstrings/man/create_dirs.Rd |only filesstrings-1.1.0/filesstrings/man/currency.Rd |only filesstrings-1.1.0/filesstrings/man/extend_char_vec.Rd |only filesstrings-1.1.0/filesstrings/man/extract_numbers.Rd |only filesstrings-1.1.0/filesstrings/man/filesstrings-defunct.Rd |only filesstrings-1.1.0/filesstrings/man/filesstrings-deprecated.Rd |only filesstrings-1.1.0/filesstrings/man/give_ext.Rd |only filesstrings-1.1.0/filesstrings/man/group_close.Rd |only filesstrings-1.1.0/filesstrings/man/locate_braces.Rd |only filesstrings-1.1.0/filesstrings/man/merge_tables_on_disk.Rd |only filesstrings-1.1.0/filesstrings/man/move_files.Rd |only filesstrings-1.1.0/filesstrings/man/nice_file_nums.Rd |only filesstrings-1.1.0/filesstrings/man/nice_nums.Rd |only filesstrings-1.1.0/filesstrings/man/paste_collapse_list_elems.Rd |only filesstrings-1.1.0/filesstrings/man/paste_different_lengths.Rd |only filesstrings-1.1.0/filesstrings/man/put_in_pos.Rd |only filesstrings-1.1.0/filesstrings/man/remove_dirs.Rd |only filesstrings-1.1.0/filesstrings/man/remove_filename_spaces.Rd |only filesstrings-1.1.0/filesstrings/man/remove_quoted.Rd |only filesstrings-1.1.0/filesstrings/man/rename_with_nums.Rd |only filesstrings-1.1.0/filesstrings/man/singleize.Rd |only filesstrings-1.1.0/filesstrings/man/str_after_nth.Rd |only filesstrings-1.1.0/filesstrings/man/str_elem.Rd |only filesstrings-1.1.0/filesstrings/man/str_list_nth_elems.Rd |only filesstrings-1.1.0/filesstrings/man/str_list_remove_empties.Rd |only filesstrings-1.1.0/filesstrings/man/str_nth_instance_indices.Rd |only filesstrings-1.1.0/filesstrings/man/str_paste_elems.Rd |only filesstrings-1.1.0/filesstrings/man/str_split_by_nums.Rd |only filesstrings-1.1.0/filesstrings/man/str_split_camel_case.Rd |only filesstrings-1.1.0/filesstrings/man/str_to_vec.Rd |only filesstrings-1.1.0/filesstrings/man/str_with_patterns.Rd |only filesstrings-1.1.0/filesstrings/man/trim_anything.Rd |only filesstrings-1.1.0/filesstrings/man/unitize_dirs.Rd |only filesstrings-1.1.0/filesstrings/src/RcppExports.cpp | 90 +- filesstrings-1.1.0/filesstrings/src/strings.cpp |only filesstrings-1.1.0/filesstrings/tests/testthat/test_RcppExports.R | 15 filesstrings-1.1.0/filesstrings/tests/testthat/test_strings.R | 2 filesstrings-1.1.0/filesstrings/vignettes/files.Rmd | 28 filesstrings-1.1.0/filesstrings/vignettes/strings.Rmd | 52 - 100 files changed, 697 insertions(+), 581 deletions(-)
Title: Excerpt Structuring Comments from Your Code File and Set a Table
of Contents
Description: This is an R interface to the
python package 'excerpts' (<https://pypi.python.org/pypi/excerpts>).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <adc-r@arcor.de>
Diff between excerptr versions 1.3.0 dated 2017-06-22 and 1.3.1 dated 2017-07-08
excerptr-1.3.0/excerptr/inst/excerpts/docs/doxygen |only excerptr-1.3.1/excerptr/DESCRIPTION | 6 - excerptr-1.3.1/excerptr/MD5 | 13 +- excerptr-1.3.1/excerptr/NEWS.md | 10 + excerptr-1.3.1/excerptr/README.md | 9 + excerptr-1.3.1/excerptr/inst/doc/excerptr_Introduction.html | 62 ++++-------- excerptr-1.3.1/excerptr/inst/tests/testthat/test_basic.R | 49 +++++---- excerptr-1.3.1/excerptr/tests/testthat/test_basic.R | 49 +++++---- 8 files changed, 98 insertions(+), 100 deletions(-)
Title: Help for Writing Unit Tests Based on Function Examples
Description: Take the examples written in your documentation of functions and
use them to create shells (skeletons which must be manually completed by
the user) of test files to be tested with the 'testthat' package.
Author: Rory Nolan [aut, cre],
Sergi Padilla-Parra [ths]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between exampletestr versions 0.4.0 dated 2017-04-12 and 1.0.0 dated 2017-07-08
DESCRIPTION | 16 +++--- MD5 | 34 +++++++------- NAMESPACE | 2 NEWS.md | 47 ++++++++++++++++--- R/exampletestr.R | 4 + R/exemplar.R | 51 +++++++++------------ R/utils.R | 2 README.md | 3 - build/vignette.rds |binary inst/doc/exampletestr.html | 14 ++--- inst/extdata/exampletestr.R | 1 inst/extdata/exemplar.R | 75 +++++++++++++++---------------- inst/extdata/test_exemplar_uncompleted.R | 7 +- inst/extdata/utils.R | 2 man/extract_examples.Rd | 4 - man/make_test_shell.Rd | 5 +- man/make_tests_shells_file.Rd | 9 +-- tests/testthat/test_exemplar.R | 19 +++---- 18 files changed, 163 insertions(+), 132 deletions(-)
Title: Modeling Earthquake Data Using ETAS Model
Description: Fits the space-time Epidemic Type Aftershock Sequence
(ETAS) model to earthquake catalogs using a stochastic declustering
approach. The ETAS model is a spatio-temporal marked point process
model and a special case of the Hawkes process. The package is based
on a Fortran program by Jiancang Zhuang
(available at <http://bemlar.ism.ac.jp/zhuang/software.html>),
which is modified and translated into C++ and C such that it
can be called from R. Parallel computing with OpenMP is possible
on supported platforms.
Author: Abdollah Jalilian [aut, cre], Jiancang Zhuang [ctb]
Maintainer: Abdollah Jalilian <jalilian@razi.ac.ir>
Diff between ETAS versions 0.4.1 dated 2017-02-15 and 0.4.3 dated 2017-07-08
ETAS-0.4.1/ETAS/src/Makevars |only ETAS-0.4.3/ETAS/DESCRIPTION | 16 ETAS-0.4.3/ETAS/MD5 | 17 - ETAS-0.4.3/ETAS/NAMESPACE | 1 ETAS-0.4.3/ETAS/R/etas.R | 12 ETAS-0.4.3/ETAS/R/resid.etas.R | 6 ETAS-0.4.3/ETAS/README.md |only ETAS-0.4.3/ETAS/src/Makevars.in |only ETAS-0.4.3/ETAS/src/RcppExports.cpp | 22 + ETAS-0.4.3/ETAS/src/fit.c | 2 ETAS-0.4.3/ETAS/src/fitMP.cpp | 592 +++++++++++++++++------------------- 11 files changed, 343 insertions(+), 325 deletions(-)
Title: Evaluation of Modeling without Information Leakage
Description: A toolbox for designing and evaluating predictive models with
resampling methods. The aim of this package is to provide a simple and
efficient general framework for working with any type of prediction
problem, be it classification, regression or survival analysis, that is
easy to extend and adapt to your specific setting. Some commonly used
methods for classification, regression and survival analysis are included.
Author: Christofer Backlin [aut, cre],
Mats Gustafsson [aut]
Maintainer: Christofer Backlin <emil@christofer.backlin.se>
Diff between emil versions 2.2.6 dated 2016-06-21 and 2.2.8 dated 2017-07-08
emil-2.2.6/emil/NEWS.md |only emil-2.2.8/emil/DESCRIPTION | 10 - emil-2.2.8/emil/MD5 | 208 ++++++++++++------------- emil-2.2.8/emil/NAMESPACE | 26 ++- emil-2.2.8/emil/R/RcppExports.R | 8 emil-2.2.8/emil/R/RcppWrappers.r | 3 emil-2.2.8/emil/R/helpers.r | 6 emil-2.2.8/emil/R/learning-curve.r | 8 emil-2.2.8/emil/R/lm.r | 1 emil-2.2.8/emil/R/modeling.r | 1 emil-2.2.8/emil/R/pamr.r | 1 emil-2.2.8/emil/R/plotting.r | 4 emil-2.2.8/emil/R/resampling.r | 2 emil-2.2.8/emil/R/reshape-result.r | 9 - emil-2.2.8/emil/R/survival.r | 1 emil-2.2.8/emil/man/as.modeling_procedure.Rd | 1 emil-2.2.8/emil/man/dichotomize.Rd | 7 emil-2.2.8/emil/man/error_fun.Rd | 11 - emil-2.2.8/emil/man/evaluate.Rd | 7 emil-2.2.8/emil/man/factor_to_logical.Rd | 1 emil-2.2.8/emil/man/fill.Rd | 1 emil-2.2.8/emil/man/fit.Rd | 7 emil-2.2.8/emil/man/fit_caret.Rd | 1 emil-2.2.8/emil/man/fit_cforest.Rd | 7 emil-2.2.8/emil/man/fit_coxph.Rd | 7 emil-2.2.8/emil/man/fit_glmnet.Rd | 9 - emil-2.2.8/emil/man/fit_lda.Rd | 7 emil-2.2.8/emil/man/fit_lm.Rd | 7 emil-2.2.8/emil/man/fit_naive_bayes.Rd | 1 emil-2.2.8/emil/man/fit_pamr.Rd | 7 emil-2.2.8/emil/man/fit_qda.Rd | 7 emil-2.2.8/emil/man/fit_randomForest.Rd | 7 emil-2.2.8/emil/man/fit_rpart.Rd | 1 emil-2.2.8/emil/man/fit_svm.Rd | 1 emil-2.2.8/emil/man/get_color.Rd | 1 emil-2.2.8/emil/man/get_importance.Rd | 7 emil-2.2.8/emil/man/get_performance.Rd | 1 emil-2.2.8/emil/man/get_prediction.Rd | 1 emil-2.2.8/emil/man/get_response.Rd | 1 emil-2.2.8/emil/man/get_tuning.Rd | 1 emil-2.2.8/emil/man/image.resample.Rd | 9 - emil-2.2.8/emil/man/importance_glmnet.Rd | 9 - emil-2.2.8/emil/man/importance_pamr.Rd | 7 emil-2.2.8/emil/man/importance_randomForest.Rd | 7 emil-2.2.8/emil/man/impute.Rd | 7 emil-2.2.8/emil/man/indent.Rd | 1 emil-2.2.8/emil/man/index_fit.Rd | 7 emil-2.2.8/emil/man/is_blank.Rd | 1 emil-2.2.8/emil/man/is_constant.Rd | 1 emil-2.2.8/emil/man/is_multi_procedure.Rd | 1 emil-2.2.8/emil/man/learning_curve.Rd | 7 emil-2.2.8/emil/man/list_method.Rd | 1 emil-2.2.8/emil/man/log_message.Rd | 1 emil-2.2.8/emil/man/mode.Rd | 1 emil-2.2.8/emil/man/modeling_procedure.Rd | 7 emil-2.2.8/emil/man/na_index.Rd | 1 emil-2.2.8/emil/man/name_procedure.Rd | 1 emil-2.2.8/emil/man/neg_gmpa.Rd | 7 emil-2.2.8/emil/man/nice_axis.Rd | 1 emil-2.2.8/emil/man/nice_box.Rd | 1 emil-2.2.8/emil/man/nice_require.Rd | 1 emil-2.2.8/emil/man/notify_once.Rd | 1 emil-2.2.8/emil/man/pipe.Rd | 1 emil-2.2.8/emil/man/plot.Surv.Rd | 1 emil-2.2.8/emil/man/plot.learning_curve.Rd | 1 emil-2.2.8/emil/man/pre_factor_to_logical.Rd | 1 emil-2.2.8/emil/man/pre_impute.Rd | 3 emil-2.2.8/emil/man/pre_impute_df.Rd | 1 emil-2.2.8/emil/man/pre_impute_knn.Rd | 1 emil-2.2.8/emil/man/pre_log_message.Rd | 7 emil-2.2.8/emil/man/pre_pamr.Rd | 7 emil-2.2.8/emil/man/pre_process.Rd | 19 +- emil-2.2.8/emil/man/predict.model.Rd | 7 emil-2.2.8/emil/man/predict_caret.Rd | 1 emil-2.2.8/emil/man/predict_cforest.Rd | 7 emil-2.2.8/emil/man/predict_coxph.Rd | 7 emil-2.2.8/emil/man/predict_glmnet.Rd | 9 - emil-2.2.8/emil/man/predict_lda.Rd | 7 emil-2.2.8/emil/man/predict_lm.Rd | 7 emil-2.2.8/emil/man/predict_naive_bayes.Rd | 7 emil-2.2.8/emil/man/predict_pamr.Rd | 7 emil-2.2.8/emil/man/predict_qda.Rd | 7 emil-2.2.8/emil/man/predict_randomForest.Rd | 7 emil-2.2.8/emil/man/predict_rpart.Rd | 1 emil-2.2.8/emil/man/predict_svm.Rd | 1 emil-2.2.8/emil/man/print.preprocessed_data.Rd | 1 emil-2.2.8/emil/man/pvalue.Rd | 7 emil-2.2.8/emil/man/pvalue.coxph.Rd | 7 emil-2.2.8/emil/man/pvalue.crr.Rd | 7 emil-2.2.8/emil/man/pvalue.cuminc.Rd | 7 emil-2.2.8/emil/man/pvalue.survdiff.Rd | 7 emil-2.2.8/emil/man/resample.Rd | 11 - emil-2.2.8/emil/man/roc_curve.Rd | 5 emil-2.2.8/emil/man/select.Rd | 10 - emil-2.2.8/emil/man/subresample.Rd | 7 emil-2.2.8/emil/man/subtree.Rd | 7 emil-2.2.8/emil/man/trivial_error_rate.Rd | 1 emil-2.2.8/emil/man/tune.Rd | 13 - emil-2.2.8/emil/man/validate_data.Rd | 1 emil-2.2.8/emil/man/vlines.Rd | 3 emil-2.2.8/emil/man/weighted_error_rate.Rd | 1 emil-2.2.8/emil/src/RcppExports.cpp | 26 +-- emil-2.2.8/emil/src/init.c |only emil-2.2.8/emil/tests/testthat/test-helpers.r | 2 emil-2.2.8/emil/tests/testthat/test-modeling.r | 4 emil-2.2.8/emil/tests/testthat/test-survival.r | 4 106 files changed, 332 insertions(+), 393 deletions(-)
Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional
disaggregated indicators. So far, estimation methods comprise direct estimation
and the model-based approach Empirical Best Prediction (see "Small area
estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>),
as well as their precision estimates. The assessment of the used model
is supported by a summary and diagnostic plots. For a suitable presentation of
estimates, map plots can be easily created. Furthermore, results can easily be
exported to excel.
Author: Ann-Kristin Kreutzmann [aut],
Soeren Pannier [aut, cre],
Natalia Rojas-Perilla [aut],
Timo Schmid [aut],
Matthias Templ [aut],
Nikos Tzavidis [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>
Diff between emdi versions 1.1.0 dated 2017-05-18 and 1.1.1 dated 2017-07-08
DESCRIPTION | 10 - MD5 | 82 +++++++------ NAMESPACE | 2 NEWS.md | 8 + R/check_direct_arguments.R | 154 ++++++++++++++++++------- R/check_ebp_arguments.R | 190 +++++++++++++++++++++---------- R/check_estimators_arguments.R |only R/check_mapplot_arguments.R |only R/check_plot_arguments.R |only R/check_writeexcel_arguments.R |only R/direct_estimation.R | 90 ++++++++------ R/direct_variance.R | 67 +++++------ R/ebp.R | 65 ++++++---- R/emdiObject.R | 5 R/estimators.emdi.R | 50 +++----- R/eusilcA_pop.R | 2 R/framework_direct.R | 25 +++- R/framework_ebp.R | 12 + R/load_shape.R | 2 R/map_plot.R | 205 ++++++++++++++++++--------------- R/mse_emdi.R | 30 ++-- R/mse_estimation.R | 28 ++-- R/plot.emdi.R | 212 +++++++++++++++++------------------ R/point_emdi.R | 26 +--- R/point_estimation.R | 2 R/point_estimation_direct.R | 2 R/print.emdi.R | 6 R/summary.emdi.R | 16 +- R/write.excel.emdi.R | 103 +++++++++-------- inst/doc/vignette_emdi.pdf |binary man/direct.Rd | 80 +++++++------ man/ebp.Rd | 36 +++-- man/emdiObject.Rd | 5 man/estimators.emdi.Rd | 24 ++- man/eusilcA_pop.Rd | 2 man/head.estimators.emdi.Rd | 2 man/load_shapeaustria.Rd | 2 man/map_plot.Rd | 70 ++++++++--- man/plot.emdi.Rd | 32 +++-- man/subset.estimators.emdi.Rd | 4 man/summary.emdi.Rd | 10 - man/tail.estimators.emdi.Rd | 4 man/write.excel.Rd | 32 ++--- tests/testthat/test_mse_estimation.R | 80 ++++++------- 44 files changed, 1039 insertions(+), 738 deletions(-)
Title: Run 'roxygen2' on (Chunks of) Single Code Files
Description: Have you ever been tempted to create 'roxygen2'-style documentation
comments for one of your functions that was not part of one of your
packages (yet)?
This is exactly what this package is about: running 'roxygen2' on
(chunks of) a single code file.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <adc-r@arcor.de>
Diff between document versions 1.2.0 dated 2017-06-01 and 1.2.1 dated 2017-07-08
document-1.2.0/document/inst/tests/document_unit_test.txt |only document-1.2.0/document/tests/document_unit_test.txt |only document-1.2.1/document/DESCRIPTION | 6 document-1.2.1/document/MD5 | 18 +- document-1.2.1/document/NEWS.md | 7 document-1.2.1/document/R/document.R | 2 document-1.2.1/document/R/man.R | 8 + document-1.2.1/document/README.md | 7 document-1.2.1/document/inst/doc/Introduction_to_document.html | 75 +++------- document-1.2.1/document/inst/tests/runit.R | 4 document-1.2.1/document/tests/runit.R | 4 11 files changed, 58 insertions(+), 73 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 1.2.4 dated 2016-10-05 and 1.2.5 dated 2017-07-08
DeLorean-1.2.4/DeLorean/R/magda.r |only DeLorean-1.2.4/DeLorean/man/magda.find.orderings.Rd |only DeLorean-1.2.5/DeLorean/DESCRIPTION | 12 DeLorean-1.2.5/DeLorean/MD5 | 247 +++++----- DeLorean-1.2.5/DeLorean/NAMESPACE | 3 DeLorean-1.2.5/DeLorean/NEWS.md | 6 DeLorean-1.2.5/DeLorean/R/model.r | 97 ++- DeLorean-1.2.5/DeLorean/R/robustness.r | 2 DeLorean-1.2.5/DeLorean/build/vignette.rds |binary DeLorean-1.2.5/DeLorean/inst/doc/DeLorean.R | 4 DeLorean-1.2.5/DeLorean/inst/doc/DeLorean.Rmd | 6 DeLorean-1.2.5/DeLorean/inst/doc/DeLorean.html | 52 +- DeLorean-1.2.5/DeLorean/inst/scripts/DeLorean-Guo.Rmd | 4 DeLorean-1.2.5/DeLorean/inst/scripts/DeLorean-Trapnell.Rmd | 4 DeLorean-1.2.5/DeLorean/inst/scripts/Kouno-DeLorean.Rmd | 4 DeLorean-1.2.5/DeLorean/inst/scripts/McDavid-DeLorean.Rmd | 21 DeLorean-1.2.5/DeLorean/inst/scripts/McDavid-profiles.eps |only DeLorean-1.2.5/DeLorean/inst/scripts/Shalek-DeLorean.Rmd | 8 DeLorean-1.2.5/DeLorean/inst/scripts/Tang-DeLorean.Rmd | 4 DeLorean-1.2.5/DeLorean/inst/scripts/Windram-DeLorean.Rmd | 6 DeLorean-1.2.5/DeLorean/inst/scripts/complexity.Rmd | 8 DeLorean-1.2.5/DeLorean/inst/scripts/config.R | 12 DeLorean-1.2.5/DeLorean/man/DeLorean.Rd | 1 DeLorean-1.2.5/DeLorean/man/Rhat.plot.Rd | 1 DeLorean-1.2.5/DeLorean/man/adjust.by.cell.sizes.Rd | 1 DeLorean-1.2.5/DeLorean/man/alpha.for.rug.Rd | 1 DeLorean-1.2.5/DeLorean/man/analyse.noise.levels.Rd | 1 DeLorean-1.2.5/DeLorean/man/analyse.variance.Rd | 1 DeLorean-1.2.5/DeLorean/man/anders.huber.cell.sizes.Rd | 1 DeLorean-1.2.5/DeLorean/man/aov.dl.Rd | 1 DeLorean-1.2.5/DeLorean/man/avg.par.samples.Rd | 1 DeLorean-1.2.5/DeLorean/man/calc.inducing.pseudotimes.Rd | 1 DeLorean-1.2.5/DeLorean/man/calc.roughness.Rd | 1 DeLorean-1.2.5/DeLorean/man/centralise.Rd | 1 DeLorean-1.2.5/DeLorean/man/cmp.profiles.plot.Rd | 1 DeLorean-1.2.5/DeLorean/man/compile.model.Rd | 1 DeLorean-1.2.5/DeLorean/man/cov.all.genes.conditioned.Rd | 1 DeLorean-1.2.5/DeLorean/man/cov.calc.dists.Rd | 1 DeLorean-1.2.5/DeLorean/man/cov.calc.dl.dists.Rd | 1 DeLorean-1.2.5/DeLorean/man/cov.calc.gene.Rd | 1 DeLorean-1.2.5/DeLorean/man/cov.calc.gene.conditioned.Rd | 1 DeLorean-1.2.5/DeLorean/man/cov.matern.32.Rd | 1 DeLorean-1.2.5/DeLorean/man/cov.periodise.Rd | 1 DeLorean-1.2.5/DeLorean/man/create.ordering.ll.fn.Rd | 1 DeLorean-1.2.5/DeLorean/man/de.lorean.Rd | 1 DeLorean-1.2.5/DeLorean/man/de.lorean.stylesheet.Rd | 1 DeLorean-1.2.5/DeLorean/man/default.num.cores.Rd | 1 DeLorean-1.2.5/DeLorean/man/dim.de.lorean.Rd | 1 DeLorean-1.2.5/DeLorean/man/estimate.cell.sizes.Rd | 1 DeLorean-1.2.5/DeLorean/man/estimate.hyper.Rd | 1 DeLorean-1.2.5/DeLorean/man/examine.convergence.Rd | 1 DeLorean-1.2.5/DeLorean/man/expected.sample.var.Rd | 1 DeLorean-1.2.5/DeLorean/man/expr.data.plot.Rd | 1 DeLorean-1.2.5/DeLorean/man/filter.cells.Rd | 12 DeLorean-1.2.5/DeLorean/man/filter.genes.Rd | 12 DeLorean-1.2.5/DeLorean/man/filter_cells.Rd |only DeLorean-1.2.5/DeLorean/man/filter_genes.Rd |only DeLorean-1.2.5/DeLorean/man/find.best.tau.Rd | 1 DeLorean-1.2.5/DeLorean/man/find.good.ordering.Rd | 1 DeLorean-1.2.5/DeLorean/man/find.smooth.tau.Rd | 1 DeLorean-1.2.5/DeLorean/man/fit.dl.Rd | 1 DeLorean-1.2.5/DeLorean/man/fit.held.out.Rd | 1 DeLorean-1.2.5/DeLorean/man/fit.model.Rd | 1 DeLorean-1.2.5/DeLorean/man/fit.model.sample.Rd | 1 DeLorean-1.2.5/DeLorean/man/fit.model.vb.Rd | 1 DeLorean-1.2.5/DeLorean/man/gaussian.condition.Rd | 1 DeLorean-1.2.5/DeLorean/man/gene.covariances.Rd | 1 DeLorean-1.2.5/DeLorean/man/get.posterior.mean.Rd | 1 DeLorean-1.2.5/DeLorean/man/gp.log.marg.like.Rd | 1 DeLorean-1.2.5/DeLorean/man/gp.predict.Rd | 1 DeLorean-1.2.5/DeLorean/man/gp.predictions.df.Rd | 1 DeLorean-1.2.5/DeLorean/man/guo.expr.Rd | 3 DeLorean-1.2.5/DeLorean/man/held.out.melt.Rd | 1 DeLorean-1.2.5/DeLorean/man/held.out.posterior.Rd | 1 DeLorean-1.2.5/DeLorean/man/held.out.posterior.by.variation.Rd | 1 DeLorean-1.2.5/DeLorean/man/held.out.posterior.filter.Rd | 1 DeLorean-1.2.5/DeLorean/man/held.out.posterior.join.Rd | 1 DeLorean-1.2.5/DeLorean/man/held.out.select.genes.Rd | 1 DeLorean-1.2.5/DeLorean/man/inducing.covariance.Rd | 1 DeLorean-1.2.5/DeLorean/man/init.orderings.vs.pseudotimes.plot.Rd | 1 DeLorean-1.2.5/DeLorean/man/is.de.lorean.Rd | 1 DeLorean-1.2.5/DeLorean/man/knit.report.Rd | 1 DeLorean-1.2.5/DeLorean/man/kouno.expr.Rd | 3 DeLorean-1.2.5/DeLorean/man/make.fit.valid.Rd | 1 DeLorean-1.2.5/DeLorean/man/make.init.fn.Rd | 1 DeLorean-1.2.5/DeLorean/man/make.predictions.Rd | 1 DeLorean-1.2.5/DeLorean/man/marg.like.plot.Rd | 1 DeLorean-1.2.5/DeLorean/man/melt.expr.Rd | 1 DeLorean-1.2.5/DeLorean/man/mutate.profile.data.Rd | 3 DeLorean-1.2.5/DeLorean/man/optimise.best.sample.Rd | 1 DeLorean-1.2.5/DeLorean/man/ordering.block.move.Rd | 1 DeLorean-1.2.5/DeLorean/man/ordering.improve.Rd | 1 DeLorean-1.2.5/DeLorean/man/ordering.invert.Rd | 1 DeLorean-1.2.5/DeLorean/man/ordering.is.valid.Rd | 1 DeLorean-1.2.5/DeLorean/man/ordering.maximise.Rd | 1 DeLorean-1.2.5/DeLorean/man/ordering.metropolis.hastings.Rd | 1 DeLorean-1.2.5/DeLorean/man/ordering.move.Rd | 1 DeLorean-1.2.5/DeLorean/man/ordering.random.block.move.Rd | 1 DeLorean-1.2.5/DeLorean/man/ordering.random.move.Rd | 1 DeLorean-1.2.5/DeLorean/man/ordering.test.score.Rd | 1 DeLorean-1.2.5/DeLorean/man/orderings.plot.Rd | 1 DeLorean-1.2.5/DeLorean/man/partition.de.lorean.Rd | 1 DeLorean-1.2.5/DeLorean/man/permute.df.Rd | 1 DeLorean-1.2.5/DeLorean/man/permuted.roughness.Rd | 1 DeLorean-1.2.5/DeLorean/man/plot.add.expr.Rd | 1 DeLorean-1.2.5/DeLorean/man/plot.add.mean.and.variance.Rd | 1 DeLorean-1.2.5/DeLorean/man/plot.de.lorean.Rd | 1 DeLorean-1.2.5/DeLorean/man/plot.held.out.posterior.Rd | 1 DeLorean-1.2.5/DeLorean/man/prepare.for.stan.Rd | 1 DeLorean-1.2.5/DeLorean/man/print.de.lorean.Rd | 1 DeLorean-1.2.5/DeLorean/man/process.posterior.Rd | 1 DeLorean-1.2.5/DeLorean/man/profiles.plot.Rd | 1 DeLorean-1.2.5/DeLorean/man/pseudotime.plot.Rd | 1 DeLorean-1.2.5/DeLorean/man/pseudotimes.from.orderings.Rd | 1 DeLorean-1.2.5/DeLorean/man/pseudotimes.pair.plot.Rd | 1 DeLorean-1.2.5/DeLorean/man/report.file.Rd | 1 DeLorean-1.2.5/DeLorean/man/roughness.of.permutations.Rd | 1 DeLorean-1.2.5/DeLorean/man/roughness.of.sample.Rd | 1 DeLorean-1.2.5/DeLorean/man/roughness.test.Rd | 1 DeLorean-1.2.5/DeLorean/man/roughnesses.plot.Rd | 1 DeLorean-1.2.5/DeLorean/man/seriation.find.orderings.Rd | 1 DeLorean-1.2.5/DeLorean/man/tau.offsets.plot.Rd | 1 DeLorean-1.2.5/DeLorean/man/test.fit.Rd | 1 DeLorean-1.2.5/DeLorean/man/test.mh.Rd | 1 DeLorean-1.2.5/DeLorean/man/test.robustness.de.lorean.Rd | 1 DeLorean-1.2.5/DeLorean/man/windram.expr.Rd | 3 DeLorean-1.2.5/DeLorean/vignettes/DeLorean.Rmd | 6 127 files changed, 291 insertions(+), 347 deletions(-)
More information about dataPreparation at CRAN
Permanent link
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii)
Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v)
Matrix functions, (vi) Projector and canonical efficiency functions, and (vii)
Miscellaneous functions. There is a vignette describing how to use the
Design functions for randomizing and assessing designs available in the file
'daeDesignNotes.pdf'. The ANOVA functions facilitate the extraction of
information when the 'Error' function has been used in the call to 'aov'.
Author: Chris Brien <Chris.Brien@unisa.edu.au>.
Maintainer: Chris Brien <Chris.Brien@unisa.edu.au>
Diff between dae versions 2.7-20 dated 2016-09-16 and 3.0-04 dated 2017-07-08
dae-2.7-20/dae/R/design.plot.r |only dae-2.7-20/dae/R/designPlot.r |only dae-2.7-20/dae/R/fac.layout.r |only dae-2.7-20/dae/R/proj.canon.v5.r |only dae-2.7-20/dae/R/projs.canon.v4.r |only dae-2.7-20/dae/inst/doc/daeDesignRandomization.pdf |only dae-2.7-20/dae/man/Ameasures.Rd |only dae-2.7-20/dae/man/blockboundary.plot.Rd |only dae-2.7-20/dae/man/design.plot.Rd |only dae-2.7-20/dae/man/efficiencies.p2canon.Rd |only dae-2.7-20/dae/man/efficiencies.pcanon.Rd |only dae-2.7-20/dae/man/projs.canon.Rd |only dae-2.7-20/dae/man/projs.structure.Rd |only dae-3.0-04/dae/DESCRIPTION | 18 +- dae-3.0-04/dae/MD5 | 165 +++++++++++++-------- dae-3.0-04/dae/NAMESPACE | 26 +++ dae-3.0-04/dae/R/Interaction.ABC.Plot.r | 11 - dae-3.0-04/dae/R/NoReps.r | 63 ++++---- dae-3.0-04/dae/R/S3methodsDeprecations.r |only dae-3.0-04/dae/R/dae.utilties.r | 40 +++++ dae-3.0-04/dae/R/daeAttach.r |only dae-3.0-04/dae/R/designPlot.v2.r |only dae-3.0-04/dae/R/designRandomize.r |only dae-3.0-04/dae/R/diagnostic.checking.r | 29 +-- dae-3.0-04/dae/R/fac.functions.r | 97 +++++++----- dae-3.0-04/dae/R/fac.layout.v3.r |only dae-3.0-04/dae/R/mat.functions.r | 109 +++++++++++++ dae-3.0-04/dae/R/proj.r | 120 ++++++++------- dae-3.0-04/dae/R/projs.canon.v5.r |only dae-3.0-04/dae/R/projs2.canon.v5.r |only dae-3.0-04/dae/R/pstructure.v2.r |only dae-3.0-04/dae/build/partial.rdb |binary dae-3.0-04/dae/data/BIBDWheat.dat.rda |only dae-3.0-04/dae/data/Casuarina.dat.rda |only dae-3.0-04/dae/data/Exp249.mplot.des.rda |only dae-3.0-04/dae/data/LatticeSquare_t49.des.rda |only dae-3.0-04/dae/data/McIntyreTMV.dat.rda |only dae-3.0-04/dae/data/Oats.dat.rda |only dae-3.0-04/dae/data/Sensory3PhaseShort.dat.rda |only dae-3.0-04/dae/inst/NEWS.Rd | 61 +++++++ dae-3.0-04/dae/inst/doc/dae-manual.pdf |binary dae-3.0-04/dae/inst/doc/daeDesignNotes.pdf |only dae-3.0-04/dae/man/BIBDWheat.dat.Rd |only dae-3.0-04/dae/man/Casuarina.dat.Rd |only dae-3.0-04/dae/man/Exp249.mplot.des.Rd |only dae-3.0-04/dae/man/LatticeSquare_t49.des.Rd |only dae-3.0-04/dae/man/McIntyreTMV.dat.Rd |only dae-3.0-04/dae/man/Oats.dat.Rd |only dae-3.0-04/dae/man/Sensory3Phase.dat.Rd | 14 + dae-3.0-04/dae/man/Zncsspline.Rd |only dae-3.0-04/dae/man/as.data.frame.pstructure.Rd |only dae-3.0-04/dae/man/blockboundaryPlot.Rd | 3 dae-3.0-04/dae/man/dae-deprecated.Rd | 13 + dae-3.0-04/dae/man/dae-package.Rd | 96 ++++++++++-- dae-3.0-04/dae/man/daeTips.Rd |only dae-3.0-04/dae/man/decomp.relate.Rd | 14 - dae-3.0-04/dae/man/designAmeasures.Rd |only dae-3.0-04/dae/man/designAnatomy.Rd |only dae-3.0-04/dae/man/designLatinSqrSys.Rd | 2 dae-3.0-04/dae/man/designPlot.Rd | 62 +++++-- dae-3.0-04/dae/man/designRandomize.Rd |only dae-3.0-04/dae/man/efficiencies.Rd |only dae-3.0-04/dae/man/efficiency.criteria.Rd | 12 - dae-3.0-04/dae/man/elements.Rd | 1 dae-3.0-04/dae/man/extab.Rd | 4 dae-3.0-04/dae/man/fac.divide.Rd | 2 dae-3.0-04/dae/man/marginality.Rd |only dae-3.0-04/dae/man/mat.I.Rd | 1 dae-3.0-04/dae/man/mat.J.Rd | 1 dae-3.0-04/dae/man/mat.Vpred.Rd | 4 dae-3.0-04/dae/man/mat.ar1.Rd | 5 dae-3.0-04/dae/man/mat.ar2.Rd | 7 dae-3.0-04/dae/man/mat.ar3.Rd | 5 dae-3.0-04/dae/man/mat.arma.Rd | 5 dae-3.0-04/dae/man/mat.banded.Rd | 3 dae-3.0-04/dae/man/mat.dirprod.Rd | 1 dae-3.0-04/dae/man/mat.dirsum.Rd | 1 dae-3.0-04/dae/man/mat.exp.Rd | 4 dae-3.0-04/dae/man/mat.gau.Rd |only dae-3.0-04/dae/man/mat.ma1.Rd | 7 dae-3.0-04/dae/man/mat.ma2.Rd | 5 dae-3.0-04/dae/man/mat.ncssvar.Rd |only dae-3.0-04/dae/man/mat.sar.Rd |only dae-3.0-04/dae/man/mat.sar2.Rd | 5 dae-3.0-04/dae/man/no.reps.Rd | 2 dae-3.0-04/dae/man/p2canon.object.Rd |only dae-3.0-04/dae/man/pcanon.object.Rd |only dae-3.0-04/dae/man/power.exp.Rd | 5 dae-3.0-04/dae/man/print.aliasing.Rd |only dae-3.0-04/dae/man/print.pstructure.Rd |only dae-3.0-04/dae/man/print.summary.p2canon.Rd | 15 + dae-3.0-04/dae/man/print.summary.pcanon.Rd | 14 + dae-3.0-04/dae/man/proj2.combine.Rd | 12 - dae-3.0-04/dae/man/proj2.efficiency.Rd | 12 - dae-3.0-04/dae/man/proj2.eigen.Rd | 14 - dae-3.0-04/dae/man/projs.2canon.Rd | 46 +---- dae-3.0-04/dae/man/projs.combine.p2canon.Rd | 12 - dae-3.0-04/dae/man/pstructure.formula.Rd |only dae-3.0-04/dae/man/pstructure.object.Rd |only dae-3.0-04/dae/man/strength.Rd | 6 dae-3.0-04/dae/man/summary.p2canon.Rd | 16 +- dae-3.0-04/dae/man/summary.pcanon.Rd | 66 +++++--- dae-3.0-04/dae/tests |only 103 files changed, 841 insertions(+), 395 deletions(-)
Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable observing of the climate
system by providing Essential Climate Variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of seven
National Meteorological and Hydrological Services.
The 'cmsaf' R-package provides a small collection of R-functions, which are
inspired by the Climate Data Operators ('cdo'). This gives the opportunity to
analyse and manipulate CM SAF data without the need of installing cdo.
The 'cmsaf' R-package is tested for CM SAF NetCDF data, which are structured
in three-dimensional arrays (longitude, latitude, time) on a rectangular grid.
Layered CM SAF data have to be converted with the provided 'levbox_mergetime()'
function. The 'cmsaf' R-package functions have only minor checks for deviations
from the recommended data structure, and give only few specific error messages.
Thus, there is no warranty of accurate results.
Scripts for an easy application of the functions are provided at the CM SAF homepage
(<http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html>).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.7.2 dated 2017-03-14 and 1.8.0 dated 2017-07-08
DESCRIPTION | 11 +- MD5 | 220 ++++++++++++++++++++++++------------------------ NAMESPACE | 3 R/box_mergetime.R | 109 ++++++++++++++++------- R/cmsaf.add.R | 53 +++++++---- R/cmsaf.addc.R | 72 +++++++++------ R/cmsaf.div.R | 74 +++++++++++++--- R/cmsaf.divc.R | 106 ++++++++++++++++------- R/cmsaf.mul.R | 74 ++++++++++++---- R/cmsaf.mulc.R | 106 ++++++++++++++++------- R/cmsaf.sub.R | 133 +++++++++++++++++++++++------ R/cmsaf.subc.R | 106 ++++++++++++++++------- R/dayrange.R | 42 ++++++--- R/divdpm.R | 46 ++++++---- R/extract.level.R | 54 +++++++---- R/extract.period.R | 44 ++++++--- R/fldmax.R | 54 +++++++---- R/fldmean.R | 44 ++++++--- R/fldmin.R | 44 ++++++--- R/levbox_mergetime.R | 54 +++++++---- R/mon.anomaly.R | 91 ++++++++++++------- R/monmax.R | 40 ++++++-- R/monmean.R | 40 ++++++-- R/monmin.R | 40 ++++++-- R/monsd.R | 40 ++++++-- R/monsum.R | 40 ++++++-- R/muldpm.R | 88 +++++++++++-------- R/multimonmean.R | 44 ++++++--- R/multimonsum.R | 42 ++++++--- R/remapbil.R | 55 +++++++----- R/seas.anomaly.R | 133 +++++++++++++++++------------ R/seasmean.R | 40 ++++++-- R/sellonlatbox.R | 54 +++++++---- R/selmon.R | 54 +++++++---- R/selperiod.R | 54 +++++++---- R/selpoint.R | 57 ++++++++---- R/selpoint.multi.R |only R/seltime.R | 56 +++++++----- R/selyear.R | 54 +++++++---- R/timmax.R | 50 +++++++--- R/timmean.R | 40 ++++++-- R/timmin.R | 50 +++++++--- R/timsd.R | 50 +++++++--- R/trend.R | 195 ++++++++++++++++++++++++++++++------------ R/wfldmean.R | 54 +++++++---- R/year.anomaly.R | 82 +++++++++++++---- R/yearmean.R | 50 +++++++--- R/yearsum.R | 50 +++++++--- R/ymonmax.R | 50 +++++++--- R/ymonmean.R | 50 +++++++--- R/ymonmin.R | 40 ++++++-- R/ymonsd.R | 50 +++++++--- R/ymonsum.R | 51 +++++++---- R/yseasmax.R | 44 ++++++--- R/yseasmean.R | 52 +++++++---- R/yseasmin.R | 42 ++++++--- R/yseassd.R | 52 +++++++---- man/box_mergetime.Rd | 6 + man/cmsaf-package.Rd | 4 man/cmsaf.add.Rd | 6 + man/cmsaf.addc.Rd | 6 + man/cmsaf.div.Rd | 6 + man/cmsaf.divc.Rd | 6 + man/cmsaf.mul.Rd | 6 + man/cmsaf.mulc.Rd | 6 + man/cmsaf.sub.Rd | 6 + man/cmsaf.subc.Rd | 6 + man/dayrange.Rd | 6 + man/divdpm.Rd | 6 + man/extract.level.Rd | 6 + man/extract.period.Rd | 14 +-- man/fldmax.Rd | 6 + man/fldmean.Rd | 6 + man/fldmin.Rd | 6 + man/levbox_mergetime.Rd | 6 + man/mon.anomaly.Rd | 6 + man/monmax.Rd | 6 + man/monmean.Rd | 6 + man/monmin.Rd | 6 + man/monsd.Rd | 6 + man/monsum.Rd | 6 + man/muldpm.Rd | 6 + man/multimonmean.Rd | 6 + man/multimonsum.Rd | 6 + man/remapbil.Rd | 6 + man/seas.anomaly.Rd | 6 + man/seasmean.Rd | 6 + man/sellonlatbox.Rd | 6 + man/selmon.Rd | 6 + man/selperiod.Rd | 6 + man/selpoint.Rd | 6 + man/selpoint.multi.Rd |only man/seltime.Rd | 6 + man/selyear.Rd | 6 + man/timmax.Rd | 6 + man/timmean.Rd | 6 + man/timmin.Rd | 6 + man/timsd.Rd | 6 + man/trend.Rd | 14 ++- man/wfldmean.Rd | 6 + man/year.anomaly.Rd | 6 + man/yearmean.Rd | 6 + man/yearsum.Rd | 6 + man/ymonmax.Rd | 6 + man/ymonmean.Rd | 6 + man/ymonmin.Rd | 6 + man/ymonsd.Rd | 6 + man/ymonsum.Rd | 6 + man/yseasmax.Rd | 6 + man/yseasmean.Rd | 6 + man/yseasmin.Rd | 6 + man/yseassd.Rd | 6 + 112 files changed, 2657 insertions(+), 1204 deletions(-)
Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a
non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the
integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out
Genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style
plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>
Diff between CMplot versions 3.2.0 dated 2017-03-20 and 3.2.1 dated 2017-07-08
DESCRIPTION | 10 - MD5 | 6 R/CMplot.r | 375 +++++++++++++++++++++++++++----------------------- man/CMplot-package.Rd | 21 ++ 4 files changed, 231 insertions(+), 181 deletions(-)
Title: Variable Selection for Gaussian Model-Based Clustering
Description: Variable selection for Gaussian model-based clustering as implemented in the 'mclust' package. The methodology allows to find the (locally) optimal subset of variables in a data set that have group/cluster information. A greedy or headlong search can be used, either in a forward-backward or backward-forward direction, with or without sub-sampling at the hierarchical clustering stage for starting 'mclust' models. By default the algorithm uses a sequential search, but parallelisation is also available.
Author: Nema Dean [aut],
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between clustvarsel versions 2.3 dated 2017-02-24 and 2.3.1 dated 2017-07-08
DESCRIPTION | 13 ++++++------- MD5 | 22 +++++++++++----------- R/clustvarsel.R | 6 +++++- R/clvarselgrbkw.R | 3 ++- R/clvarselgrfwd.R | 6 ++---- R/clvarselhlbkw.R | 3 ++- R/clvarselhlfwd.R | 3 ++- build/vignette.rds |binary inst/NEWS | 3 +++ inst/doc/clustvarsel.html | 42 ++++++++++++++++++++++++------------------ man/clustvarsel-internal.Rd | 8 ++++---- man/clustvarsel.Rd | 2 +- 12 files changed, 62 insertions(+), 49 deletions(-)
Title: Fix Data and Create Report Tables from Different Objects
Description: Fixes data errors in numerical, factor and date variables, checks data quality and performs report tables from models and summaries.
Author: Victoria Fornes Ferrer, David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>
Diff between clickR versions 0.2.0 dated 2017-02-20 and 0.2.9 dated 2017-07-08
DESCRIPTION | 10 +-- MD5 | 80 +++++++++++++++--------------- NAMESPACE | 4 + NEWS | 48 ++++++++++++++++++ R/descriptive.R | 113 ++++++++++++++++++++++++++++++++++++++----- README.md |only man/check_quality.Rd | 1 man/descriptivo.Rd | 5 - man/extreme_values.Rd | 1 man/fix.dates.Rd | 1 man/fix.factors.Rd | 1 man/fix.levels.Rd | 1 man/fix.numerics.Rd | 8 +-- man/ipboxplot.Rd | 1 man/is.it.Rd | 1 man/kill.factors.Rd |only man/make_csv_table.Rd | 1 man/make_latex_table.Rd | 1 man/make_table.Rd | 1 man/make_word_table.Rd | 1 man/matrixPaste.Rd | 1 man/may.numeric.Rd | 1 man/mine.plot.Rd | 1 man/mtapply.Rd | 1 man/nice_names.Rd |only man/numeros.Rd | 1 man/peek.Rd |only man/report.Rd | 1 man/report.betareg.Rd | 1 man/report.clm.Rd | 1 man/report.clmm.Rd | 1 man/report.coxph.Rd | 1 man/report.data.frame.Rd | 1 man/report.factor.Rd | 1 man/report.glm.Rd | 1 man/report.glmerMod.Rd | 1 man/report.lm.Rd | 1 man/report.lmerMod.Rd | 1 man/report.lqmm.Rd | 1 man/report.merModLmerTest.Rd | 1 man/report.numeric.Rd | 1 man/report.rq.Rd | 1 man/ttrue.Rd | 1 43 files changed, 205 insertions(+), 95 deletions(-)
Title: Computerized Adaptive Testing for Survey Research
Description: Provides methods of computerized adaptive testing for survey researchers. Includes functionality for data fit with the classic item response methods including the latent trait model, Birnbaum`s three parameter model, the graded response, and the generalized partial credit model. Additionally, includes several ability parameter estimation and item selection routines. During item selection, all calculations are done in compiled C++ code.
Author: Jacob Montgomery [aut],
Erin Rossiter [aut, cre]
Maintainer: Erin Rossiter <erinrossiter@wustl.edu>
Diff between catSurv versions 1.0.2 dated 2017-06-26 and 1.0.3 dated 2017-07-08
DESCRIPTION | 6 MD5 | 40 - NAMESPACE | 2 NEWS.md | 11 R/RcppExports.R | 93 +++ man/estimateThetas.Rd |only man/simulateThetas.Rd |only src/Cat.cpp | 214 +++++-- src/Cat.h | 10 src/EPVSelector.cpp | 25 src/Estimator.cpp | 952 ++++++++++++++++++++++------------- src/Estimator.h | 28 - src/MAPEstimator.cpp | 4 src/Prior.cpp | 55 +- src/Prior.h | 30 - src/QuestionSet.cpp | 191 +++++-- src/QuestionSet.h | 7 src/RcppExports.cpp | 24 src/WLEEstimator.cpp | 32 - src/init.c | 4 src/main.cpp | 106 +++ tests/testthat/test-estimateThetas.R |only tests/testthat/test-simulateThetas.R |only 23 files changed, 1320 insertions(+), 514 deletions(-)
Title: Bias Reduction with Missing Binary Response
Description: Provides two main functions, il() and fil(). The il() function implements the EM algorithm developed by Ibrahim and Lipsitz (1996) <DOI:10.2307/2533068> to estimate the parameters of a logistic regression model with the missing response when the missing data mechanism is nonignorable. The fil() function implements the algorithm proposed by Maity et. al. (2017+) <https://github.com/arnabkrmaity/brlrmr> to reduce the bias produced by the method of Ibrahim and Lipsitz (1996) <DOI:10.2307/2533068>.
Author: Arnab Maity [aut, cre],
Vivek Pradhan [ctb],
Ujjwal Das [ctb]
Maintainer: Arnab Maity <akumar@stat.tamu.edu>
Diff between brlrmr versions 0.1.2 dated 2017-06-09 and 0.1.3 dated 2017-07-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/fil.R | 41 +++++++++++++++++++++++++++-------------- 3 files changed, 32 insertions(+), 19 deletions(-)
Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R
without printing the content of graphics windows to an embosser of some kind. This
is not as immediate as is required for efficient access to statistical output.
The functions here are created so that blind people can make even better use
of R. This includes the text descriptions of graphs, convenience functions
to replace the functionality offered in many GUI front ends, and experimental
functionality for optimising graphical content to prepare it for embossing as
tactile images.
Author: A. Jonathan R. Godfrey [aut, cre], Donal Fitzpatrick [ctb], Duncan Murdoch [ctb], Greg Snow
[ctb], Henrik Bengtsson [ctb], James Curtis [ctb], JooYoung Seo [ctb], Paul Murrell [ctb], Timothy Bilton [aut], Tony Hirst [ctb], Tsan-Kuang Lee [ctb], Volker Sorge [aut], Yihui Xie
[ctb]
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>
Diff between BrailleR versions 0.24.2 dated 2016-03-29 and 0.26.0 dated 2017-07-08
BrailleR-0.24.2/BrailleR/R/BrailleRHome.R |only BrailleR-0.24.2/BrailleR/inst/BrailleROptions |only BrailleR-0.24.2/BrailleR/inst/WriteROptions |only BrailleR-0.24.2/BrailleR/inst/css |only BrailleR-0.24.2/BrailleR/inst/foo.pandoc |only BrailleR-0.24.2/BrailleR/man/BrailleRHome.Rd |only BrailleR-0.26.0/BrailleR/DESCRIPTION | 31 BrailleR-0.26.0/BrailleR/MD5 | 229 +- BrailleR-0.26.0/BrailleR/NAMESPACE | 86 BrailleR-0.26.0/BrailleR/R/AddXMLInternal.R |only BrailleR-0.26.0/BrailleR/R/AddXMLMethod.R |only BrailleR-0.26.0/BrailleR/R/Augment.R |only BrailleR-0.26.0/BrailleR/R/AutoSpellCheck.R |only BrailleR-0.26.0/BrailleR/R/BRLThis.R | 29 BrailleR-0.26.0/BrailleR/R/BrailleRUsefulLinks.R |only BrailleR-0.26.0/BrailleR/R/BrowseSVG.R |only BrailleR-0.26.0/BrailleR/R/CleanCSV.R |only BrailleR-0.26.0/BrailleR/R/DataViewer.R | 73 BrailleR-0.26.0/BrailleR/R/Describe.R |only BrailleR-0.26.0/BrailleR/R/FindReplace.R |only BrailleR-0.26.0/BrailleR/R/GetWriteR.R |only BrailleR-0.26.0/BrailleR/R/GettingStarted.R | 116 - BrailleR-0.26.0/BrailleR/R/Internal.R | 39 BrailleR-0.26.0/BrailleR/R/JoinBlindRUG.R | 39 BrailleR-0.26.0/BrailleR/R/MakeAccessibleSVGMethod.R |only BrailleR-0.26.0/BrailleR/R/MakeAllFormats.R | 21 BrailleR-0.26.0/BrailleR/R/MakeBatch.R | 115 - BrailleR-0.26.0/BrailleR/R/MakeReadable.R | 61 BrailleR-0.26.0/BrailleR/R/MakeRmdFiles.R | 82 BrailleR-0.26.0/BrailleR/R/MakeRprofile.R | 24 BrailleR-0.26.0/BrailleR/R/MakeSlideShow.R | 218 +- BrailleR-0.26.0/BrailleR/R/MaskedFunctions.R | 60 BrailleR-0.26.0/BrailleR/R/NewFunction.R | 66 BrailleR-0.26.0/BrailleR/R/NonMethodFunctions.R | 28 BrailleR-0.26.0/BrailleR/R/OneFactor.R | 399 ++-- BrailleR-0.26.0/BrailleR/R/OnePredictor.R | 366 ++-- BrailleR-0.26.0/BrailleR/R/Options.R | 669 ++++--- BrailleR-0.26.0/BrailleR/R/Premier100.R | 21 BrailleR-0.26.0/BrailleR/R/PrepareWriteR.R | 52 BrailleR-0.26.0/BrailleR/R/ProcessAll.R |only BrailleR-0.26.0/BrailleR/R/R2txtExtraJG.R | 48 BrailleR-0.26.0/BrailleR/R/R2txtJG.R | 160 - BrailleR-0.26.0/BrailleR/R/RewriteSVG.R |only BrailleR-0.26.0/BrailleR/R/Rnw2Rmd.R |only BrailleR-0.26.0/BrailleR/R/SVGThis.R | 233 +- BrailleR-0.26.0/BrailleR/R/ScatterPlot.R |only BrailleR-0.26.0/BrailleR/R/SetupBrailleR.R | 106 - BrailleR-0.26.0/BrailleR/R/SpellCheck.R |only BrailleR-0.26.0/BrailleR/R/SpellCheckFiles.R |only BrailleR-0.26.0/BrailleR/R/TSPlot.R |only BrailleR-0.26.0/BrailleR/R/TextStrings.R |only BrailleR-0.26.0/BrailleR/R/ThreeFactors.R |only BrailleR-0.26.0/BrailleR/R/TwoFactors.R | 508 +++-- BrailleR-0.26.0/BrailleR/R/UniDesc.R | 494 +++-- BrailleR-0.26.0/BrailleR/R/UpdateGraph.R |only BrailleR-0.26.0/BrailleR/R/UseTemplate.R |only BrailleR-0.26.0/BrailleR/R/VIMethod1_JG.R | 395 ++-- BrailleR-0.26.0/BrailleR/R/VIMethod2_TB.R | 141 - BrailleR-0.26.0/BrailleR/R/VIMethod3_TH.R |only BrailleR-0.26.0/BrailleR/R/ViewSVG.R |only BrailleR-0.26.0/BrailleR/R/WTF.R | 152 - BrailleR-0.26.0/BrailleR/R/WhereXY.R | 107 - BrailleR-0.26.0/BrailleR/R/WriteR.R | 38 BrailleR-0.26.0/BrailleR/R/dotplots.R | 111 - BrailleR-0.26.0/BrailleR/R/history.R | 33 BrailleR-0.26.0/BrailleR/R/latest.R |only BrailleR-0.26.0/BrailleR/R/nNonMissing.R |only BrailleR-0.26.0/BrailleR/R/zzz.R | 99 - BrailleR-0.26.0/BrailleR/build/vignette.rds |binary BrailleR-0.26.0/BrailleR/inst/CITATION | 2 BrailleR-0.26.0/BrailleR/inst/MyBrailleR |only BrailleR-0.26.0/BrailleR/inst/NEWS | 86 BrailleR-0.26.0/BrailleR/inst/Python/WriteR/EditMenuEvents.pyc |only BrailleR-0.26.0/BrailleR/inst/Python/WriteR/HelpMenuEvents.pyc |only BrailleR-0.26.0/BrailleR/inst/Python/WriteR/MathInserts.pyc |only BrailleR-0.26.0/BrailleR/inst/Python/WriteR/RMarkdownEvents.pyc |only BrailleR-0.26.0/BrailleR/inst/Python/WriteR/WriteR.pyw | 888 ++++++---- BrailleR-0.26.0/BrailleR/inst/Templates |only BrailleR-0.26.0/BrailleR/inst/Web |only BrailleR-0.26.0/BrailleR/inst/doc/BrailleRHistory.html | 137 - BrailleR-0.26.0/BrailleR/inst/doc/BrailleRHistory.rmd | 37 BrailleR-0.26.0/BrailleR/inst/doc/Ex1histograms.html | 155 - BrailleR-0.26.0/BrailleR/inst/doc/Ex2BasicNumerical.html | 35 BrailleR-0.26.0/BrailleR/inst/doc/Ex3UnivariateDescription.html | 23 BrailleR-0.26.0/BrailleR/inst/doc/Ex4SingleResponseOneGroupingFactor.html | 23 BrailleR-0.26.0/BrailleR/inst/doc/GettingStarted.Rmd | 8 BrailleR-0.26.0/BrailleR/inst/doc/GettingStarted.html | 31 BrailleR-0.26.0/BrailleR/inst/doc/IntroWriteR.Rmd |only BrailleR-0.26.0/BrailleR/inst/doc/IntroWriteR.html |only BrailleR-0.26.0/BrailleR/inst/doc/qplot.R |only BrailleR-0.26.0/BrailleR/inst/doc/qplot.Rmd |only BrailleR-0.26.0/BrailleR/inst/doc/qplot.html |only BrailleR-0.26.0/BrailleR/man/AddXMLInternal.Rd |only BrailleR-0.26.0/BrailleR/man/AddXMLMethod.Rd |only BrailleR-0.26.0/BrailleR/man/AugmentMethod.Rd |only BrailleR-0.26.0/BrailleR/man/AutoSpellCheck.Rd |only BrailleR-0.26.0/BrailleR/man/BRLThis.Rd | 6 BrailleR-0.26.0/BrailleR/man/BrailleR-package.Rd | 6 BrailleR-0.26.0/BrailleR/man/BrailleRUsefulLinks.Rd |only BrailleR-0.26.0/BrailleR/man/BrowseSVG.Rd |only BrailleR-0.26.0/BrailleR/man/CleanCSV.Rd |only BrailleR-0.26.0/BrailleR/man/DataViewer.Rd | 2 BrailleR-0.26.0/BrailleR/man/FindReplace.Rd |only BrailleR-0.26.0/BrailleR/man/GetWriteR.Rd |only BrailleR-0.26.0/BrailleR/man/Internal.Rd | 9 BrailleR-0.26.0/BrailleR/man/JoinBlindRUG.Rd | 14 BrailleR-0.26.0/BrailleR/man/MakeAccessibleSVGMethod.Rd |only BrailleR-0.26.0/BrailleR/man/MakeAllFormats.Rd | 2 BrailleR-0.26.0/BrailleR/man/MakeBatch.Rd | 12 BrailleR-0.26.0/BrailleR/man/MakeRmdFiles.Rd | 17 BrailleR-0.26.0/BrailleR/man/MakeSlideShow.Rd | 11 BrailleR-0.26.0/BrailleR/man/OneFactor.Rd | 2 BrailleR-0.26.0/BrailleR/man/OnePredictor.Rd | 2 BrailleR-0.26.0/BrailleR/man/Options.Rd | 2 BrailleR-0.26.0/BrailleR/man/PrepareWriteR.Rd | 2 BrailleR-0.26.0/BrailleR/man/R2txtJG.Rd | 4 BrailleR-0.26.0/BrailleR/man/SVGThis.Rd | 10 BrailleR-0.26.0/BrailleR/man/ScatterPlot.Rd |only BrailleR-0.26.0/BrailleR/man/SetOptions.Rd | 2 BrailleR-0.26.0/BrailleR/man/SpellCheck.Rd |only BrailleR-0.26.0/BrailleR/man/SpellCheckFiles.Rd |only BrailleR-0.26.0/BrailleR/man/TSPlot.Rd |only BrailleR-0.26.0/BrailleR/man/ThreeFactors.Rd |only BrailleR-0.26.0/BrailleR/man/UpdateGraph.Rd |only BrailleR-0.26.0/BrailleR/man/VI.Rd | 35 BrailleR-0.26.0/BrailleR/man/VI.ggplot.Rd |only BrailleR-0.26.0/BrailleR/man/ViewSVG.Rd |only BrailleR-0.26.0/BrailleR/man/WhereXY.Rd | 2 BrailleR-0.26.0/BrailleR/man/boxplot.Rd | 6 BrailleR-0.26.0/BrailleR/man/dotplot.Rd | 2 BrailleR-0.26.0/BrailleR/man/hist.Rd | 4 BrailleR-0.26.0/BrailleR/man/unfinished.Rd | 2 BrailleR-0.26.0/BrailleR/vignettes/BrailleRHistory.rmd | 37 BrailleR-0.26.0/BrailleR/vignettes/BrailleRPublications.bib | 86 BrailleR-0.26.0/BrailleR/vignettes/GettingStarted.Rmd | 8 BrailleR-0.26.0/BrailleR/vignettes/IntroWriteR.Rmd |only BrailleR-0.26.0/BrailleR/vignettes/qplot.Rmd |only 137 files changed, 4331 insertions(+), 2828 deletions(-)
Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary Kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: François Rousset [aut, cre, cph],
Raphaël Leblois [ctb]
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between blackbox versions 1.0.18 dated 2017-02-02 and 1.1.0 dated 2017-07-08
DESCRIPTION | 10 ++--- MD5 | 75 ++++++++++++++++++++++--------------------- NAMESPACE | 5 +- R/LRTfn.R | 13 +++++-- R/blackbox.R | 32 ++++++++++-------- R/buildFONKgpointls.R | 53 ++++++++++++++++++------------ R/calc1DCIs.R | 30 +++++++++++++---- R/calc1Dprofiles.R | 12 ++++++ R/calcPredictorOK.R | 10 ++--- R/calcProfileLR.R | 2 + R/calcProfileOK.R | 2 - R/calcgridRelProfile.R | 4 ++ R/canonize.R | 59 ++++++++++++++++++++------------- R/findglobalMLE.R | 6 +++ R/formatName.R | 43 ++++++++++++++++++++---- R/fromFONKtoanyspace.R | 6 ++- R/generateNewPoints.R | 2 - R/generateNextpointsfromCI.R | 1 R/gridfn.R | 10 +++++ R/massBarycenter.R | 2 - R/optimWrapper.R | 4 +- R/prepareData.R | 2 - R/profile.R | 22 ++++++------ R/profileFn.R | 2 - R/providefullhull.R | 10 +++++ R/rawProfiles.R | 9 ++++- R/redundant.addVeq.R | 6 +-- R/resetCHull.R | 4 +- R/sampleByResp.R | 19 ++++++++-- R/toDgmuFromCanonical.R |only R/toTgmuFromCanonical.R |only R/tofullKrigingspace.R | 24 ++++++++++++- R/volTriangulation.R | 2 - R/writeFinalInfo.R | 18 ++++++---- inst/NEWS.Rd | 24 +++++++++++++ man/bboptim.Rd | 54 ++++++++++++++++++++---------- man/blackbox-internal.Rd | 2 + man/options.Rd | 8 ---- src/init.c |only tests/testthat/test-1D.R | 2 - 40 files changed, 398 insertions(+), 191 deletions(-)
Title: Binary Graph Analysis Tools
Description: Tools to analyze binary graph objects.
Author: Terrence Brooks, Berkley Shands, Skye Buckner-Petty, Patricio S. La Rosa, Elena Deych, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between bingat versions 1.2.2 dated 2016-01-15 and 1.3 dated 2017-07-08
bingat-1.2.2/bingat/man/BinGAT-internal.Rd |only bingat-1.2.2/bingat/man/BinGAT-package.Rd |only bingat-1.2.2/bingat/man/gaConsensus.Rd |only bingat-1.3/bingat/DESCRIPTION | 14 +- bingat-1.3/bingat/MD5 | 78 ++++++----- bingat-1.3/bingat/NAMESPACE | 12 + bingat-1.3/bingat/NEWS | 92 +++++++------ bingat-1.3/bingat/R/array2mat.R | 25 ++- bingat-1.3/bingat/R/calcDistance.R | 26 +-- bingat-1.3/bingat/R/estGStar.R | 14 +- bingat-1.3/bingat/R/estLogLik.R | 58 +++++--- bingat-1.3/bingat/R/estMLE.R | 8 - bingat-1.3/bingat/R/estTau.R | 52 ++++--- bingat-1.3/bingat/R/full2lt.R | 11 - bingat-1.3/bingat/R/gaConsensus.R | 66 --------- bingat-1.3/bingat/R/gaCreation.R |only bingat-1.3/bingat/R/gaPlot.R |only bingat-1.3/bingat/R/gaScoring.R |only bingat-1.3/bingat/R/genAlg.R |only bingat-1.3/bingat/R/genAlgConsensus.R |only bingat-1.3/bingat/R/getGibbsMixture.R | 179 ++++++++++++-------------- bingat-1.3/bingat/R/getLoglikeMixture.R | 55 ++++---- bingat-1.3/bingat/R/getNumEdges.R | 24 +-- bingat-1.3/bingat/R/getNumNodes.R | 36 ++--- bingat-1.3/bingat/R/glmReg.R | 66 ++++----- bingat-1.3/bingat/R/glrtPvalue.R | 126 ++++++++++-------- bingat-1.3/bingat/R/glrtReg.R | 13 - bingat-1.3/bingat/R/graphNetworkPlot.R | 52 +++---- bingat-1.3/bingat/R/list2mat.R | 23 +-- bingat-1.3/bingat/R/lrtPvalue.R | 153 +++++++++++----------- bingat-1.3/bingat/R/lt2full.R | 15 +- bingat-1.3/bingat/R/pairedPvalue.R | 120 +++++++++++------ bingat-1.3/bingat/R/plotHeatmap.R | 35 ++--- bingat-1.3/bingat/R/plotMDS.R | 155 +++++++++++++--------- bingat-1.3/bingat/R/rGibbs.R | 60 ++++---- bingat-1.3/bingat/R/testGoF.R | 196 ++++++++++++++--------------- bingat-1.3/bingat/R/vec2mat.R | 29 ++-- bingat-1.3/bingat/man/bingat-internal.Rd |only bingat-1.3/bingat/man/bingat-package.Rd |only bingat-1.3/bingat/man/estLogLik.Rd | 5 bingat-1.3/bingat/man/genAlg.Rd |only bingat-1.3/bingat/man/genAlgConsensus.Rd |only bingat-1.3/bingat/man/glrtPvalue.Rd | 26 ++- bingat-1.3/bingat/man/lrtPvalue.Rd | 19 +- bingat-1.3/bingat/man/pairedPvalue.Rd | 24 ++- bingat-1.3/bingat/man/plotMDS.Rd | 16 +- 46 files changed, 991 insertions(+), 892 deletions(-)
Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill
Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>
Diff between BIGDAWG versions 1.5.5 dated 2016-08-30 and 1.13 dated 2017-07-08
BIGDAWG-1.13/BIGDAWG/DESCRIPTION | 27 BIGDAWG-1.13/BIGDAWG/MD5 | 140 +-- BIGDAWG-1.13/BIGDAWG/NEWS | 325 ++++--- BIGDAWG-1.13/BIGDAWG/R/A.R | 4 BIGDAWG-1.13/BIGDAWG/R/A_ExonPtnAlign_functions.R | 514 +++++------ BIGDAWG-1.13/BIGDAWG/R/A_wrapper.R | 156 +-- BIGDAWG-1.13/BIGDAWG/R/BIGDAWG.R | 973 +++++++++++----------- BIGDAWG-1.13/BIGDAWG/R/CheckRelease.R | 118 +- BIGDAWG-1.13/BIGDAWG/R/HWE_wrapper.R | 64 - BIGDAWG-1.13/BIGDAWG/R/H_MC.R |only BIGDAWG-1.13/BIGDAWG/R/H_support_functions.R | 89 +- BIGDAWG-1.13/BIGDAWG/R/H_wrapper_MC.R |only BIGDAWG-1.13/BIGDAWG/R/L.R | 3 BIGDAWG-1.13/BIGDAWG/R/L_wrapper.R | 126 +- BIGDAWG-1.13/BIGDAWG/R/check_functions.R | 421 ++++----- BIGDAWG-1.13/BIGDAWG/R/data.R | 24 BIGDAWG-1.13/BIGDAWG/R/general_functions.R | 879 +++++++++++-------- BIGDAWG-1.13/BIGDAWG/R/sysdata.rda |binary BIGDAWG-1.13/BIGDAWG/R/update_wrapper.R | 199 ++-- BIGDAWG-1.13/BIGDAWG/build/vignette.rds |binary BIGDAWG-1.13/BIGDAWG/inst/doc/BIGDAWG.Rmd | 504 +++++------ BIGDAWG-1.13/BIGDAWG/inst/doc/BIGDAWG.html | 553 ++++++------ BIGDAWG-1.13/BIGDAWG/man/A.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/A.wrapper.Rd | 77 - BIGDAWG-1.13/BIGDAWG/man/AA.df.check.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/AAtable.builder.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/AlignObj.Create.Rd | 43 BIGDAWG-1.13/BIGDAWG/man/AlignObj.Update.Rd | 43 BIGDAWG-1.13/BIGDAWG/man/AlignmentFilter.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/BIGDAWG.Rd | 22 BIGDAWG-1.13/BIGDAWG/man/CheckAlleles.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/CheckHLA.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/CheckLoci.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/CheckLociName.Rd |only BIGDAWG-1.13/BIGDAWG/man/CheckRelease.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/DRB345.flag.Rd |only BIGDAWG-1.13/BIGDAWG/man/DRB345.parser.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/DRB345.zygosity.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/EVSremoval.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/Err.Log.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/ExonPtnAlign.Create.Rd | 39 BIGDAWG-1.13/BIGDAWG/man/ExonPtnList.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/GetField.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/GetFiles.Rd | 35 BIGDAWG-1.13/BIGDAWG/man/H.MC.Rd |only BIGDAWG-1.13/BIGDAWG/man/H.MC.wrapper.Rd |only BIGDAWG-1.13/BIGDAWG/man/HLA_data.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/HWE.ChiSq.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/HWE.Rd | 39 BIGDAWG-1.13/BIGDAWG/man/HWE.wrapper.Rd | 47 - BIGDAWG-1.13/BIGDAWG/man/L.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/L.wrapper.Rd | 67 - BIGDAWG-1.13/BIGDAWG/man/MergeData_Output.Rd |only BIGDAWG-1.13/BIGDAWG/man/PgrpExtract.Rd | 39 BIGDAWG-1.13/BIGDAWG/man/PgrpFormat.Rd | 39 BIGDAWG-1.13/BIGDAWG/man/PreCheck.Rd | 55 - BIGDAWG-1.13/BIGDAWG/man/RunChiSq.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/TableMaker.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/UpdateRelease.Rd | 41 BIGDAWG-1.13/BIGDAWG/man/buildHAPnames.Rd |only BIGDAWG-1.13/BIGDAWG/man/buildHAPsets.Rd |only BIGDAWG-1.13/BIGDAWG/man/cci.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/cci.pval.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/cci.pval.list.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/getAllele.Count.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/getCS.Mat.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/getCS.stat.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/getHap.Rd | 3 BIGDAWG-1.13/BIGDAWG/man/getObsFreq.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/make2x2.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/makeComb.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/rmABstrings.Rd | 1 BIGDAWG-1.13/BIGDAWG/man/summaryGeno.2.Rd |only BIGDAWG-1.13/BIGDAWG/vignettes/BIGDAWG.Rmd | 504 +++++------ BIGDAWG-1.5.5/BIGDAWG/R/H.R |only BIGDAWG-1.5.5/BIGDAWG/R/H_wrapper.R |only BIGDAWG-1.5.5/BIGDAWG/man/H.Rd |only BIGDAWG-1.5.5/BIGDAWG/man/H.wrapper.Rd |only 78 files changed, 3288 insertions(+), 2953 deletions(-)
Title: Bibliometric and Co-Citation Analysis Tool
Description: Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from SCOPUS (<http://scopus.com>) and
Clarivate Analytics Web of Science (<http://www.webofknowledge.com/>) databases, performing bibliometric analysis
and building data matrices for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut],
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 1.6 dated 2017-05-09 and 1.7 dated 2017-07-08
bibliometrix-1.6/bibliometrix/R/couplingSimilarity.R |only bibliometrix-1.6/bibliometrix/man/couplingSimilarity.Rd |only bibliometrix-1.7/bibliometrix/COPYING | 38 +- bibliometrix-1.7/bibliometrix/DESCRIPTION | 12 bibliometrix-1.7/bibliometrix/MD5 | 162 +++++----- bibliometrix-1.7/bibliometrix/NAMESPACE | 11 bibliometrix-1.7/bibliometrix/NEWS | 13 bibliometrix-1.7/bibliometrix/R/biblio.R | 3 bibliometrix-1.7/bibliometrix/R/biblioAnalysis.R | 4 bibliometrix-1.7/bibliometrix/R/biblioNetwork.R | 9 bibliometrix-1.7/bibliometrix/R/biblio_df.R | 3 bibliometrix-1.7/bibliometrix/R/conceptualStructure.R | 75 ++++ bibliometrix-1.7/bibliometrix/R/convert2df.R | 7 bibliometrix-1.7/bibliometrix/R/countries.R | 3 bibliometrix-1.7/bibliometrix/R/garfield.R | 3 bibliometrix-1.7/bibliometrix/R/histPlot.R | 2 bibliometrix-1.7/bibliometrix/R/isiCollection.R | 3 bibliometrix-1.7/bibliometrix/R/localCitations.R | 9 bibliometrix-1.7/bibliometrix/R/networkPlot.R | 52 ++- bibliometrix-1.7/bibliometrix/R/normalizeSimilarity.R |only bibliometrix-1.7/bibliometrix/R/scientometrics.R | 3 bibliometrix-1.7/bibliometrix/R/scientometrics_text.R | 3 bibliometrix-1.7/bibliometrix/R/scopusCollection.R | 3 bibliometrix-1.7/bibliometrix/R/stopwords.R | 3 bibliometrix-1.7/bibliometrix/R/summary.bibliometrix.R | 2 bibliometrix-1.7/bibliometrix/R/termExtraction.R | 4 bibliometrix-1.7/bibliometrix/R/thematicEvolution.R |only bibliometrix-1.7/bibliometrix/R/thematicMap.R |only bibliometrix-1.7/bibliometrix/build/vignette.rds |binary bibliometrix-1.7/bibliometrix/data/biblio.rda |binary bibliometrix-1.7/bibliometrix/data/biblio_df.rda |binary bibliometrix-1.7/bibliometrix/data/countries.rda |binary bibliometrix-1.7/bibliometrix/data/garfield.rda |binary bibliometrix-1.7/bibliometrix/data/isiCollection.rda |binary bibliometrix-1.7/bibliometrix/data/scientometrics.rda |binary bibliometrix-1.7/bibliometrix/data/scientometrics_text.rda |binary bibliometrix-1.7/bibliometrix/data/scopusCollection.rda |binary bibliometrix-1.7/bibliometrix/data/stopwords.rda |binary bibliometrix-1.7/bibliometrix/inst/CITATION | 2 bibliometrix-1.7/bibliometrix/inst/doc/bibliometrix-vignette.R | 4 bibliometrix-1.7/bibliometrix/inst/doc/bibliometrix-vignette.Rmd | 6 bibliometrix-1.7/bibliometrix/inst/doc/bibliometrix-vignette.html | 80 ++-- bibliometrix-1.7/bibliometrix/man/Hindex.Rd | 1 bibliometrix-1.7/bibliometrix/man/KeywordGrowth.Rd | 1 bibliometrix-1.7/bibliometrix/man/biblio.Rd | 6 bibliometrix-1.7/bibliometrix/man/biblioAnalysis.Rd | 3 bibliometrix-1.7/bibliometrix/man/biblioNetwork.Rd | 1 bibliometrix-1.7/bibliometrix/man/biblio_df.Rd | 6 bibliometrix-1.7/bibliometrix/man/citations.Rd | 1 bibliometrix-1.7/bibliometrix/man/cocMatrix.Rd | 1 bibliometrix-1.7/bibliometrix/man/conceptualStructure.Rd | 10 bibliometrix-1.7/bibliometrix/man/convert2df.Rd | 3 bibliometrix-1.7/bibliometrix/man/countries.Rd | 6 bibliometrix-1.7/bibliometrix/man/dominance.Rd | 1 bibliometrix-1.7/bibliometrix/man/duplicatedMatching.Rd | 1 bibliometrix-1.7/bibliometrix/man/garfield.Rd | 6 bibliometrix-1.7/bibliometrix/man/histNetwork.Rd | 1 bibliometrix-1.7/bibliometrix/man/histPlot.Rd | 1 bibliometrix-1.7/bibliometrix/man/idByAuthor.Rd | 1 bibliometrix-1.7/bibliometrix/man/isi2df.Rd | 3 bibliometrix-1.7/bibliometrix/man/isiCollection.Rd | 6 bibliometrix-1.7/bibliometrix/man/isibib2df.Rd | 3 bibliometrix-1.7/bibliometrix/man/keywordAssoc.Rd | 1 bibliometrix-1.7/bibliometrix/man/localCitations.Rd | 1 bibliometrix-1.7/bibliometrix/man/lotka.Rd | 1 bibliometrix-1.7/bibliometrix/man/mergeDbSources.Rd | 1 bibliometrix-1.7/bibliometrix/man/metaTagExtraction.Rd | 1 bibliometrix-1.7/bibliometrix/man/networkPlot.Rd | 24 + bibliometrix-1.7/bibliometrix/man/normalizeSimilarity.Rd |only bibliometrix-1.7/bibliometrix/man/plot.bibliometrix.Rd | 1 bibliometrix-1.7/bibliometrix/man/readFiles.Rd | 1 bibliometrix-1.7/bibliometrix/man/retrievalByAuthorID.Rd | 1 bibliometrix-1.7/bibliometrix/man/scientometrics.Rd | 6 bibliometrix-1.7/bibliometrix/man/scientometrics_text.Rd | 6 bibliometrix-1.7/bibliometrix/man/scopus2df.Rd | 3 bibliometrix-1.7/bibliometrix/man/scopusCollection.Rd | 6 bibliometrix-1.7/bibliometrix/man/stopwords.Rd | 6 bibliometrix-1.7/bibliometrix/man/summary.bibliometrix.Rd | 1 bibliometrix-1.7/bibliometrix/man/tableTag.Rd | 1 bibliometrix-1.7/bibliometrix/man/termExtraction.Rd | 5 bibliometrix-1.7/bibliometrix/man/thematicEvolution.Rd |only bibliometrix-1.7/bibliometrix/man/thematicMap.Rd |only bibliometrix-1.7/bibliometrix/man/timeslice.Rd | 1 bibliometrix-1.7/bibliometrix/man/trim.Rd | 1 bibliometrix-1.7/bibliometrix/man/trim.leading.Rd | 1 bibliometrix-1.7/bibliometrix/vignettes/bibliometrix-vignette.Rmd | 6 86 files changed, 377 insertions(+), 279 deletions(-)
Title: Bayesian Random-Effects Meta-Analysis
Description: A collection of functions allowing to derive the posterior distribution of the two parameters in a random-effects meta-analysis, and providing functionality to evaluate joint and marginal posterior probability distributions, predictive distributions, shrinkage effects, etc.
Author: Christian Roever [aut, cre], Tim Friede [ctb]
Maintainer: Christian Roever <christian.roever@med.uni-goettingen.de>
Diff between bayesmeta versions 1.4 dated 2017-02-17 and 1.5 dated 2017-07-08
bayesmeta-1.4/bayesmeta/data/Cochran1954.R |only bayesmeta-1.4/bayesmeta/data/CrinsEtAl2014.R |only bayesmeta-1.4/bayesmeta/data/GoralczykEtAl2011.R |only bayesmeta-1.4/bayesmeta/data/HinksEtAl2010.R |only bayesmeta-1.4/bayesmeta/data/Peto1980.R |only bayesmeta-1.4/bayesmeta/data/RoweEtAl2000.R |only bayesmeta-1.4/bayesmeta/data/Rubin1981.R |only bayesmeta-1.4/bayesmeta/data/SidikJonkman2007.R |only bayesmeta-1.4/bayesmeta/data/SnedecorCochran.R |only bayesmeta-1.5/bayesmeta/DESCRIPTION | 8 bayesmeta-1.5/bayesmeta/MD5 | 47 - bayesmeta-1.5/bayesmeta/NAMESPACE | 11 bayesmeta-1.5/bayesmeta/R/bayesmeta.R | 227 +++++-- bayesmeta-1.5/bayesmeta/build/vignette.rds |binary bayesmeta-1.5/bayesmeta/data/Cochran1954.rda |only bayesmeta-1.5/bayesmeta/data/CrinsEtAl2014.rda |only bayesmeta-1.5/bayesmeta/data/GoralczykEtAl2011.rda |only bayesmeta-1.5/bayesmeta/data/HinksEtAl2010.rda |only bayesmeta-1.5/bayesmeta/data/Peto1980.rda |only bayesmeta-1.5/bayesmeta/data/RoweEtAl2000.rda |only bayesmeta-1.5/bayesmeta/data/Rubin1981.rda |only bayesmeta-1.5/bayesmeta/data/SidikJonkman2007.rda |only bayesmeta-1.5/bayesmeta/data/SnedecorCochran.rda |only bayesmeta-1.5/bayesmeta/inst/doc/bayesmeta.html | 615 +++++++++++++------- bayesmeta-1.5/bayesmeta/man/Rubin1981.Rd | 2 bayesmeta-1.5/bayesmeta/man/SidikJonkman2007.Rd | 10 bayesmeta-1.5/bayesmeta/man/bayesmeta-package.Rd | 4 bayesmeta-1.5/bayesmeta/man/bayesmeta.Rd | 37 + bayesmeta-1.5/bayesmeta/man/dhalflogistic.Rd |only bayesmeta-1.5/bayesmeta/man/dhalfnormal.Rd | 13 bayesmeta-1.5/bayesmeta/man/forest.bayesmeta.Rd | 6 bayesmeta-1.5/bayesmeta/man/forestplot.bayesmeta.Rd | 12 bayesmeta-1.5/bayesmeta/man/normalmixture.Rd | 8 bayesmeta-1.5/bayesmeta/man/plot.bayesmeta.Rd | 13 34 files changed, 716 insertions(+), 297 deletions(-)
Title: Hierarchical Bayesian ANOVA Models
Description: It covers several Bayesian Analysis of Variance (BANOVA) models used in analysis of experimental designs in which both within- and between- subjects factors are manipulated. They can be applied to data that are common in the behavioral and social sciences. The package includes: Hierarchical Bayes ANOVA models with normal response, t response, Binomial(Bernoulli) response, Poisson response, ordered multinomial response and multinomial response variables. All models accommodate unobserved heterogeneity by including a normal distribution of the parameters across individuals. Outputs of the package include tables of sums of squares, effect sizes and p-values, and tables of predictions, which are easily interpretable for behavioral and social researchers. The floodlight analysis and mediation analysis based on these models are also provided. BANOVA uses Stan and JAGS as the computational platform.
Author: Chen Dong, Michel Wedel
Maintainer: Chen Dong <cdong@math.umd.edu>
Diff between BANOVA versions 0.8 dated 2016-12-16 and 0.9 dated 2017-07-08
BANOVA-0.8/BANOVA/man/BANOVA.Bern.Rd |only BANOVA-0.8/BANOVA/man/BANOVA.Bin.Rd |only BANOVA-0.9/BANOVA/DESCRIPTION | 14 BANOVA-0.9/BANOVA/MD5 | 188 - BANOVA-0.9/BANOVA/NAMESPACE | 83 BANOVA-0.9/BANOVA/NEWS | 59 BANOVA-0.9/BANOVA/R/BANOVA.Bern.R | 4 BANOVA-0.9/BANOVA/R/BANOVA.BernNormal.R | 189 + BANOVA-0.9/BANOVA/R/BANOVA.Bin.R | 4 BANOVA-0.9/BANOVA/R/BANOVA.BinNormal.R | 195 + BANOVA-0.9/BANOVA/R/BANOVA.MultiNormal.R | 6 BANOVA-0.9/BANOVA/R/BANOVA.NormalNormal.R | 213 + BANOVA-0.9/BANOVA/R/BANOVA.PNormal.R | 203 + BANOVA-0.9/BANOVA/R/BANOVA.TNormal.R | 179 - BANOVA-0.9/BANOVA/R/BANOVA.build.R |only BANOVA-0.9/BANOVA/R/BANOVA.floodlight.R | 32 BANOVA-0.9/BANOVA/R/BANOVA.mediation.R | 382 +-- BANOVA-0.9/BANOVA/R/BANOVA.model.R |only BANOVA-0.9/BANOVA/R/BANOVA.ordMultiNormal.R | 239 + BANOVA-0.9/BANOVA/R/BANOVA.run.R |only BANOVA-0.9/BANOVA/R/BAnova.R | 15 BANOVA-0.9/BANOVA/R/JAGSgen.PNormal.R | 34 BANOVA-0.9/BANOVA/R/JAGSgen.TNormal.R | 38 BANOVA-0.9/BANOVA/R/JAGSgen.bernNormal.R | 34 BANOVA-0.9/BANOVA/R/JAGSgen.binNormal.R | 34 BANOVA-0.9/BANOVA/R/JAGSgen.multiNormal.R | 37 BANOVA-0.9/BANOVA/R/JAGSgen.normalNormal.R | 42 BANOVA-0.9/BANOVA/R/JAGSgen.ordmultiNormal.R | 51 BANOVA-0.9/BANOVA/R/cal.mediation.effects.R | 8 BANOVA-0.9/BANOVA/R/conv.diag.R | 28 BANOVA-0.9/BANOVA/R/conv.geweke.heidel.R | 5 BANOVA-0.9/BANOVA/R/design.matrix.R | 187 - BANOVA-0.9/BANOVA/R/est.multi.R | 18 BANOVA-0.9/BANOVA/R/floodlight.analysis.R | 421 +-- BANOVA-0.9/BANOVA/R/multi.design.matrix.R | 440 ++- BANOVA-0.9/BANOVA/R/multi.predict.means.R | 232 + BANOVA-0.9/BANOVA/R/multi.print.table.means.R | 1201 ++++++--- BANOVA-0.9/BANOVA/R/pairs.R |only BANOVA-0.9/BANOVA/R/predict.BANOVA.Bern.R | 12 BANOVA-0.9/BANOVA/R/predict.BANOVA.Bin.R | 12 BANOVA-0.9/BANOVA/R/predict.BANOVA.R |only BANOVA-0.9/BANOVA/R/predict.means.R | 23 BANOVA-0.9/BANOVA/R/print.BANOVA.Bern.R | 16 BANOVA-0.9/BANOVA/R/print.BANOVA.Bin.R | 16 BANOVA-0.9/BANOVA/R/print.BANOVA.R |only BANOVA-0.9/BANOVA/R/print.BANOVA.floodlight.R | 36 BANOVA-0.9/BANOVA/R/print.BANOVA.mediation.R | 16 BANOVA-0.9/BANOVA/R/print.BANOVA.ordMultinomial.R | 20 BANOVA-0.9/BANOVA/R/print.ancova.effect.R | 14 BANOVA-0.9/BANOVA/R/print.conv.diag.R | 2 BANOVA-0.9/BANOVA/R/print.summary.BANOVA.Bern.R | 40 BANOVA-0.9/BANOVA/R/print.summary.BANOVA.Bin.R | 40 BANOVA-0.9/BANOVA/R/print.summary.BANOVA.Multinomial.R | 40 BANOVA-0.9/BANOVA/R/print.summary.BANOVA.Normal.R | 40 BANOVA-0.9/BANOVA/R/print.summary.BANOVA.Poisson.R | 40 BANOVA-0.9/BANOVA/R/print.summary.BANOVA.R |only BANOVA-0.9/BANOVA/R/print.summary.BANOVA.T.R | 40 BANOVA-0.9/BANOVA/R/print.summary.BANOVA.ordMultinomial.R | 40 BANOVA-0.9/BANOVA/R/print.table.means.R | 1689 +++++++------- BANOVA-0.9/BANOVA/R/summary.BANOVA.Bern.R | 4 BANOVA-0.9/BANOVA/R/summary.BANOVA.Bin.R | 4 BANOVA-0.9/BANOVA/R/summary.BANOVA.R |only BANOVA-0.9/BANOVA/R/table.ANCOVA.R | 418 ++- BANOVA-0.9/BANOVA/R/table.coefficients.R | 124 - BANOVA-0.9/BANOVA/R/table.predictions.R | 184 + BANOVA-0.9/BANOVA/R/trace.plot.R | 24 BANOVA-0.9/BANOVA/R/traceplot.R | 37 BANOVA-0.9/BANOVA/README.md |only BANOVA-0.9/BANOVA/inst |only BANOVA-0.9/BANOVA/man/BANOVA-package.Rd | 130 - BANOVA-0.9/BANOVA/man/BANOVA.Bernoulli.Rd |only BANOVA-0.9/BANOVA/man/BANOVA.Binomial.Rd |only BANOVA-0.9/BANOVA/man/BANOVA.Multinomial.Rd | 204 - BANOVA-0.9/BANOVA/man/BANOVA.Normal.Rd | 180 - BANOVA-0.9/BANOVA/man/BANOVA.Poisson.Rd | 6 BANOVA-0.9/BANOVA/man/BANOVA.T.Rd | 5 BANOVA-0.9/BANOVA/man/BANOVA.build.Rd |only BANOVA-0.9/BANOVA/man/BANOVA.floodlight.Rd | 6 BANOVA-0.9/BANOVA/man/BANOVA.mediation.Rd | 10 BANOVA-0.9/BANOVA/man/BANOVA.model.Rd |only BANOVA-0.9/BANOVA/man/BANOVA.ordMultinomial.Rd | 4 BANOVA-0.9/BANOVA/man/BANOVA.run.Rd |only BANOVA-0.9/BANOVA/man/BAnova.Rd | 9 BANOVA-0.9/BANOVA/man/bernlogtime.Rd | 2 BANOVA-0.9/BANOVA/man/bpndata.Rd | 118 BANOVA-0.9/BANOVA/man/colorad.Rd | 88 BANOVA-0.9/BANOVA/man/colorad2.Rd | 17 BANOVA-0.9/BANOVA/man/condstudy.Rd | 8 BANOVA-0.9/BANOVA/man/conv.diag.Rd | 10 BANOVA-0.9/BANOVA/man/goalstudy.Rd | 10 BANOVA-0.9/BANOVA/man/ipadstudy.Rd | 98 BANOVA-0.9/BANOVA/man/pairs.BANOVA.Rd |only BANOVA-0.9/BANOVA/man/table.predictions.Rd | 6 BANOVA-0.9/BANOVA/man/table.pvalues.Rd | 7 BANOVA-0.9/BANOVA/man/trace.plot.Rd | 5 BANOVA-0.9/BANOVA/src |only 96 files changed, 5126 insertions(+), 3543 deletions(-)
Title: Amazon Web Services Bundle Package
Description: A bundle of all of 'cloudyr' project <http://cloudyr.github.io/> packages for Amazon Web Services ('AWS') <https://aws.amazon.com/>. It depends upon all of the 'cloudyr' project's 'AWS' packages. It is mainly useful for installing the entire suite of packages; more likely than not you will only want to load individual packages one at a time.
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between awspack versions 0.1.2 dated 2017-07-01 and 0.1.6 dated 2017-07-08
awspack-0.1.2/awspack/R |only awspack-0.1.6/awspack/DESCRIPTION | 13 +++++++------ awspack-0.1.6/awspack/MD5 | 9 ++++----- awspack-0.1.6/awspack/NAMESPACE | 11 +++++++++++ awspack-0.1.6/awspack/NEWS.md | 16 ++++++++++++++++ awspack-0.1.6/awspack/man/awspack-package.Rd | 6 +----- 6 files changed, 39 insertions(+), 16 deletions(-)
Title: AWS SQS Client Package
Description: A simple client package for the Amazon Web Services ('AWS') Simple
Queue Service ('SQS') <https://aws.amazon.com/sqs/> 'API'.
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between aws.sqs versions 0.1.8 dated 2016-12-09 and 0.1.10 dated 2017-07-08
aws.sqs-0.1.10/aws.sqs/DESCRIPTION | 18 +++--- aws.sqs-0.1.10/aws.sqs/MD5 | 34 +++++------ aws.sqs-0.1.10/aws.sqs/NAMESPACE | 4 - aws.sqs-0.1.10/aws.sqs/NEWS.md |only aws.sqs-0.1.10/aws.sqs/R/http.R | 14 ++-- aws.sqs-0.1.10/aws.sqs/R/permissions.R | 5 - aws.sqs-0.1.10/aws.sqs/README.md | 77 ++++++++++++++------------ aws.sqs-0.1.10/aws.sqs/man/attributes.Rd | 8 +- aws.sqs-0.1.10/aws.sqs/man/aws.sqs-package.Rd | 3 - aws.sqs-0.1.10/aws.sqs/man/get_queue_url.Rd | 7 +- aws.sqs-0.1.10/aws.sqs/man/list_queues.Rd | 9 +-- aws.sqs-0.1.10/aws.sqs/man/permissions.Rd | 17 ++--- aws.sqs-0.1.10/aws.sqs/man/purge_queue.Rd | 7 +- aws.sqs-0.1.10/aws.sqs/man/queues.Rd | 7 +- aws.sqs-0.1.10/aws.sqs/man/receive_msg.Rd | 9 +-- aws.sqs-0.1.10/aws.sqs/man/send_msg.Rd | 7 +- aws.sqs-0.1.10/aws.sqs/man/sqsHTTP.Rd | 13 +--- aws.sqs-0.1.10/aws.sqs/man/visibility.Rd | 7 +- aws.sqs-0.1.8/aws.sqs/NEWS |only 19 files changed, 120 insertions(+), 126 deletions(-)
Title: AWS SNS Client Package
Description: A simple client package for the Amazon Web Services ('AWS') Simple
Notification Service ('SNS') 'API' <https://aws.amazon.com/sns/>.
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between aws.sns versions 0.1.5 dated 2016-12-08 and 0.1.7 dated 2017-07-08
aws.sns-0.1.5/aws.sns/NEWS |only aws.sns-0.1.5/aws.sns/man/add_permission.Rd |only aws.sns-0.1.7/aws.sns/DESCRIPTION | 22 ++++--- aws.sns-0.1.7/aws.sns/MD5 | 30 +++++----- aws.sns-0.1.7/aws.sns/NAMESPACE | 4 - aws.sns-0.1.7/aws.sns/NEWS.md |only aws.sns-0.1.7/aws.sns/R/http.R | 57 +++++++++----------- aws.sns-0.1.7/aws.sns/R/topic.R | 10 +-- aws.sns-0.1.7/aws.sns/README.md | 44 ++++++++------- aws.sns-0.1.7/aws.sns/man/add_topic_permission.Rd |only aws.sns-0.1.7/aws.sns/man/aws.sns-package.Rd | 3 - aws.sns-0.1.7/aws.sns/man/get_subscription_attrs.Rd | 7 +- aws.sns-0.1.7/aws.sns/man/get_topic_attrs.Rd | 7 +- aws.sns-0.1.7/aws.sns/man/list_subscriptions.Rd | 7 +- aws.sns-0.1.7/aws.sns/man/publish.Rd | 7 +- aws.sns-0.1.7/aws.sns/man/snsHTTP.Rd | 11 +-- aws.sns-0.1.7/aws.sns/man/subscriptions.Rd | 7 +- aws.sns-0.1.7/aws.sns/man/topics.Rd | 7 +- 18 files changed, 108 insertions(+), 115 deletions(-)
Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Description: Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R users.
See <http://imagej.net/Auto_Threshold> and Landini et al. (2017) <DOI:10.1111/jmi.12474>.
Author: Rory Nolan [aut, cre, trl],
Luis Alvarez [ctb],
Sergi Padilla-Parra [ctb, ths],
Gabriel Landini [ctb, cph]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between autothresholdr versions 0.5.0 dated 2017-05-17 and 0.6.0 dated 2017-07-08
autothresholdr-0.5.0/autothresholdr/man/CanBeInteger.Rd |only autothresholdr-0.5.0/autothresholdr/man/mean_pillars.Rd |only autothresholdr-0.5.0/autothresholdr/src/init.c |only autothresholdr-0.6.0/autothresholdr/DESCRIPTION | 6 autothresholdr-0.6.0/autothresholdr/MD5 | 53 - autothresholdr-0.6.0/autothresholdr/NAMESPACE | 2 autothresholdr-0.6.0/autothresholdr/NEWS.md | 50 + autothresholdr-0.6.0/autothresholdr/R/RcppExports.R | 25 autothresholdr-0.6.0/autothresholdr/R/stack_thresh.R | 113 ++- autothresholdr-0.6.0/autothresholdr/R/thresh.R | 55 - autothresholdr-0.6.0/autothresholdr/R/utils.R | 22 autothresholdr-0.6.0/autothresholdr/inst/CITATION | 2 autothresholdr-0.6.0/autothresholdr/inst/doc/autothresholdr.R | 18 autothresholdr-0.6.0/autothresholdr/inst/doc/autothresholdr.Rmd | 18 autothresholdr-0.6.0/autothresholdr/inst/doc/autothresholdr.html | 26 autothresholdr-0.6.0/autothresholdr/inst/include/autothresholdr_RcppExports.h | 19 autothresholdr-0.6.0/autothresholdr/inst/java/Auto_Threshold_R.jar |binary autothresholdr-0.6.0/autothresholdr/java/Auto_Threshold_R.class |binary autothresholdr-0.6.0/autothresholdr/java/Auto_Threshold_R.jar |binary autothresholdr-0.6.0/autothresholdr/java/Auto_Threshold_R.java | 295 +++++--- autothresholdr-0.6.0/autothresholdr/java/Auto_Threshold_original.java | 334 ++++++---- autothresholdr-0.6.0/autothresholdr/man/auto_thresh.Rd | 36 - autothresholdr-0.6.0/autothresholdr/man/mean_stack_thresh.Rd | 49 + autothresholdr-0.6.0/autothresholdr/man/med_stack_thresh.Rd |only autothresholdr-0.6.0/autothresholdr/man/sum_pillars.Rd |only autothresholdr-0.6.0/autothresholdr/src/RcppExports.cpp | 46 + autothresholdr-0.6.0/autothresholdr/src/pillar_stats.cpp | 33 autothresholdr-0.6.0/autothresholdr/tests/testthat/test_stack_thresh.R | 8 autothresholdr-0.6.0/autothresholdr/tests/testthat/test_thresh.R | 20 autothresholdr-0.6.0/autothresholdr/vignettes/autothresholdr.Rmd | 18 30 files changed, 836 insertions(+), 412 deletions(-)
More information about autothresholdr at CRAN
Permanent link
More information about Autoplotprotein at CRAN
Permanent link
Title: Visualizing Asymmetric Data
Description: Multidimensional scaling models and methods for the visualization for asymmetric data. A matrix is asymmetric if the number of rows equals the number of columns, and these rows and columns refer to the same set of objects. An example is a student migration table, where the rows correspond to the countries of origin of the students and the columns to the destination countries. This package provides the slide-vector model, a scaling model with unique dimensions and the asymscal model for asymmetric multidimensional scaling. Furthermore, a heat map for skew-symmetric data, and the decomposition of asymmetry are provided for the analysis of asymmetric tables.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>
Diff between asymmetry versions 1.2.1 dated 2017-05-15 and 1.2.2 dated 2017-07-08
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++++--------------- NAMESPACE | 4 +++- R/asymscal.R | 4 +++- R/mdsunique.R |only R/plot.mdsunique.R |only R/slidevector.R | 7 +------ R/summary.slidevector.R | 2 -- build/partial.rdb |binary inst/java/asymmetry.jar |binary man/Englishtowns.Rd | 6 +++--- man/asymscal.Rd | 5 ++++- man/asymscalexample.rd | 2 +- man/decomposition.Rd | 2 +- man/hmap.Rd | 1 + man/mdsunique.Rd |only man/plot.mdsunique.Rd |only man/plot.slidevector.Rd | 8 ++++---- man/slidevector.Rd | 9 +++++---- man/studentmigration.Rd | 2 +- 20 files changed, 51 insertions(+), 45 deletions(-)
Title: Fractional ARIMA (and Other Long Memory) Time Series Modeling
Description: Simulates, fits, and predicts long-memory and anti-persistent time
series, possibly mixed with ARMA, regression, transfer-function components.
Exact methods (MLE, forecasting, simulation) are used.
Author: JQ (Justin) Veenstra [aut, cre],
A.I. McLeod [aut]
Maintainer: JQ (Justin) Veenstra <jqveenstra@gmail.com>
Diff between arfima versions 1.4-0 dated 2017-06-20 and 1.5-0 dated 2017-07-08
arfima-1.4-0/arfima/R/Boot.ARFIMA.R |only arfima-1.4-0/arfima/R/Boot.R |only arfima-1.4-0/arfima/man/Boot.Rd |only arfima-1.4-0/arfima/man/Boot.arfima.Rd |only arfima-1.5-0/arfima/DESCRIPTION | 8 arfima-1.5-0/arfima/MD5 | 66 +- arfima-1.5-0/arfima/NAMESPACE | 3 arfima-1.5-0/arfima/R/arfima.R | 30 - arfima-1.5-0/arfima/R/arfimaFit.R | 618 +++++++++--------------- arfima-1.5-0/arfima/R/arfima_function.R | 573 ++++++++++------------ arfima-1.5-0/arfima/R/iARMA.R | 2 arfima-1.5-0/arfima/R/plot.predARFIMA.R | 92 +-- arfima-1.5-0/arfima/R/predict.ARFIMA.R | 79 --- arfima-1.5-0/arfima/R/sims.R | 116 ++-- arfima-1.5-0/arfima/R/tacf.R | 8 arfima-1.5-0/arfima/R/utilityfcns.R | 95 +-- arfima-1.5-0/arfima/R/zzz.R | 31 - arfima-1.5-0/arfima/man/AIC.arfima.Rd | 8 arfima-1.5-0/arfima/man/arfima-package.Rd | 20 arfima-1.5-0/arfima/man/arfima.Rd | 7 arfima-1.5-0/arfima/man/bestModes.Rd | 5 arfima-1.5-0/arfima/man/coef.arfima.Rd | 4 arfima-1.5-0/arfima/man/distance.Rd | 4 arfima-1.5-0/arfima/man/fitted.arfima.Rd | 4 arfima-1.5-0/arfima/man/iARFIMA.Rd | 2 arfima-1.5-0/arfima/man/plot.predarfima.Rd | 9 arfima-1.5-0/arfima/man/predict.arfima.Rd | 25 arfima-1.5-0/arfima/man/print.predarfima.Rd | 4 arfima-1.5-0/arfima/man/print.summary.arfima.Rd | 4 arfima-1.5-0/arfima/man/removeMode.Rd | 5 arfima-1.5-0/arfima/man/residuals.arfima.Rd | 4 arfima-1.5-0/arfima/man/summary.arfima.Rd | 4 arfima-1.5-0/arfima/man/tacfplot.Rd | 8 arfima-1.5-0/arfima/man/tmpyr.Rd | 11 arfima-1.5-0/arfima/man/vcov.arfima.Rd | 8 arfima-1.5-0/arfima/man/weed.Rd | 4 36 files changed, 807 insertions(+), 1054 deletions(-)
Title: Analysis with Profile Hidden Markov Models
Description: Designed for the development and application of
hidden Markov models and profile HMMs for biological sequence analysis.
Contains functions for multiple and pairwise sequence alignment,
model construction and parameter optimization, file import/export,
implementation of the forward, backward and Viterbi algorithms for
conditional sequence probabilities, tree-based sequence weighting,
and sequence simulation.
Features a wide variety of potential applications including
database searching, gene-finding and annotation, phylogenetic
analysis and sequence classification.
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Diff between aphid versions 1.0.0 dated 2017-06-24 and 1.0.1 dated 2017-07-08
aphid-1.0.0/aphid/man/whichmax.Rd |only aphid-1.0.1/aphid/DESCRIPTION | 6 +++--- aphid-1.0.1/aphid/MD5 | 17 ++++++++--------- aphid-1.0.1/aphid/R/RcppExports.R | 19 +------------------ aphid-1.0.1/aphid/R/Viterbi.R | 36 ++++++++++++++++++------------------ aphid-1.0.1/aphid/R/data.R | 2 +- aphid-1.0.1/aphid/R/derivePHMM.R | 2 +- aphid-1.0.1/aphid/R/generate.R | 12 ++++++------ aphid-1.0.1/aphid/man/casino.Rd | 2 +- aphid-1.0.1/aphid/src/ViterbiC.cpp | 35 +++++++++++++++++------------------ 10 files changed, 56 insertions(+), 75 deletions(-)
Title: Implementation of Augmented Network Log Anomaly Detection
Procedures
Description: Implements procedures to aid in detecting network log anomalies.
By combining various multivariate analytic approaches relevant to network
anomaly detection, it provides cyber analysts efficient means to detect
suspected anomalies requiring further evaluation.
Author: Bradley Boehmke [aut, cre],
Robert Gutierrez [aut],
Kenneth Bauer [ctb],
Trevor Bihl [ctb],
Cade Saie [ctb]
Maintainer: Bradley Boehmke <bradleyboehmke@gmail.com>
Diff between anomalyDetection versions 0.1.1 dated 2017-03-29 and 0.1.2 dated 2017-07-08
DESCRIPTION | 12 ++++----- MD5 | 30 ++++++++++++----------- R/bd_row.R | 6 ++-- R/block_inspect.R | 7 ++--- R/factor_analysis.R | 13 +++------- R/horns_curve.R | 15 +++++------ R/kaisers_index.R | 18 +++----------- R/mahalanobis_distance.R | 14 +++++------ R/mc_adjust.R | 39 ++++++++++++++---------------- R/pca.R | 2 - R/tabulated_state_vector.R | 38 ++++++++++++++--------------- README.md | 8 +++--- build/vignette.rds |binary inst/doc/Introduction.html | 56 ++++++++++++++++++++++---------------------- man/mahalanobis_distance.Rd | 4 +-- tools |only 16 files changed, 122 insertions(+), 140 deletions(-)
More information about anomalyDetection at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-15 1.5.1
2012-11-06 1.04
2012-10-09 1.03
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-28 3.7
2016-09-27 3.6
2014-11-26 3.5
2014-09-23 3.3