Title: Data Science Labs
Description: Datasets and functions that facilitate data analysis labs in data science courses and workshops.
Author: Rafael A. Irizarry
Maintainer: Rafael A. Irizarry <rafa@jimmy.harvard.edu>
Diff between dslabs versions 0.3.3 dated 2017-11-06 and 0.4.0 dated 2018-08-02
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++++++++++++++-- NAMESPACE | 1 + R/mnist_27.R |only R/movielens.R |only R/olive.R |only R/polls_2008.R |only R/read_mnist.R |only R/trump_tweets.R |only data/datalist |only data/mnist_27.rda |only data/movielens.rda |only data/olive.rda |only data/polls_2008.rda |only data/trump_tweets.rda |only inst/extdata/olive.csv |only inst/script/make-mnist_27.R |only inst/script/make-movielens.R |only inst/script/make-olive.R |only inst/script/make-polls_2008.R |only inst/script/make-trump_tweets.R |only man/mnist_27.Rd |only man/movielens.Rd |only man/olive.Rd |only man/polls_2008.Rd |only man/read_mnist.Rd |only man/trump_tweets.Rd |only 27 files changed, 30 insertions(+), 5 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Author: Xiaowei Zhan [aut, cre],
Dajiang Liu [aut],
Attractive Chaos [cph] (We have used the following software and made
minimal necessary changes: Tabix, Heng Li <lh3@live.co.uk> (MIT
license). We removed standard IO related functions, e.g. printf,
fprintf ; also changed its un-safe pointer arithmetics.),
Broad Institute / Massachusetts Institute of Technology [cph],
Genome Research Ltd (GRL) [cph]
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 6.0 dated 2017-05-05 and 6.1 dated 2018-08-02
seqminer-6.0/seqminer/src/IO.cpp |only seqminer-6.0/seqminer/src/IO.h |only seqminer-6.1/seqminer/DESCRIPTION | 8 ++--- seqminer-6.1/seqminer/MD5 | 32 +++++++++++------------ seqminer-6.1/seqminer/src/AnnotationOutputFile.h | 2 - seqminer-6.1/seqminer/src/BedReader.h | 2 - seqminer-6.1/seqminer/src/Codon.h | 2 - seqminer-6.1/seqminer/src/FileIO.cpp |only seqminer-6.1/seqminer/src/FileIO.h |only seqminer-6.1/seqminer/src/GeneLoader.cpp | 2 - seqminer-6.1/seqminer/src/GenomeScore.h | 2 - seqminer-6.1/seqminer/src/GenomeSequence.h | 2 - seqminer-6.1/seqminer/src/PeopleSet.cpp | 2 - seqminer-6.1/seqminer/src/PlinkInputFile.h | 2 - seqminer-6.1/seqminer/src/RangeList.cpp | 2 - seqminer-6.1/seqminer/src/SimpleMatrix.cpp | 2 - seqminer-6.1/seqminer/src/TabixData.h | 2 - seqminer-6.1/seqminer/src/VCFInputFile.cpp | 2 - seqminer-6.1/seqminer/src/VCFRecord.h | 2 - 19 files changed, 33 insertions(+), 33 deletions(-)
Title: Fast Nearest Neighbor Search Algorithms and Applications
Description: Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications
including KNN classification, regression and information measures are implemented.
Author: Alina Beygelzimer, Sham Kakadet and John Langford (cover tree library),
Sunil Arya and David Mount (ANN library 1.1.2 for the kd-tree approach), Shengqiao Li
Maintainer: Shengqiao Li <lishengqiao@yahoo.com>
Diff between FNN versions 1.1 dated 2013-07-31 and 1.1.2 dated 2018-08-02
ChangeLog | 8 ++++- DESCRIPTION | 14 ++++---- MD5 | 51 ++++++++++++++++---------------- NAMESPACE | 12 ++++--- R/KNN.R | 27 ++++++++-------- R/KNN.information.measures.R | 17 +++++----- R/OWNN.R | 11 ++++++ man/KL.dist.Rd | 2 - man/KL.divergence.Rd | 2 - man/crossentropy.Rd | 2 - man/entropy.Rd | 2 - man/get.knn.Rd | 11 +++++- man/knn.Rd | 5 +-- man/knn.cv.Rd | 5 +-- man/knn.dist.Rd | 5 +-- man/knn.index.Rd | 5 +-- man/knn.reg.Rd | 5 +-- man/mutual_information.Rd | 3 - man/ownn.rd | 2 - man/print.knnRegCV.Rd | 2 - src/KNN_ANN.cpp | 58 ++++++++++++++++++------------------ src/KNN_correlation_distance.cpp | 32 ++++++++++---------- src/KNN_cover_tree.cpp | 18 ++++++----- src/KNN_mutual_information.cpp | 62 +++++++++++++++++++-------------------- src/Makevars.win | 42 +++++++++++++------------- src/init_FNN.c |only src/label_point.h | 5 +-- 27 files changed, 221 insertions(+), 187 deletions(-)
Title: Penalized Precision Matrix Estimation via ADMM
Description: Estimates a penalized precision matrix via the alternating direction method of multipliers (ADMM) algorithm. It currently supports a general elastic-net penalty that allows for both ridge and lasso-type penalties as special cases. This package is an alternative to the 'glasso' package.
See Boyd et al (2010) <doi:10.1561/2200000016> for details regarding the estimation method.
Author: Matt Galloway [aut, cre]
Maintainer: Matt Galloway <gall0441@umn.edu>
Diff between ADMMsigma versions 2.0 dated 2018-05-31 and 2.1 dated 2018-08-02
DESCRIPTION | 11 ++-- MD5 | 112 +++++++++++++++++++++++++++++++++++++++------- NEWS.md |only R/ADMMsigma.R | 124 ++++++++++++++++++++++++++++++++-------------------- R/Parallel.R | 88 +++++++++++++++++++++--------------- R/RIDGEsigma.R | 55 +++++++++++++++-------- R/RcppExports.R | 10 ++-- build |only inst |only man/ADMMc.Rd | 4 - man/ADMMsigma.Rd | 13 ++--- man/CVP_ADMM.Rd | 8 +-- man/CVP_ADMMc.Rd | 2 man/CV_ADMMc.Rd | 2 man/RIDGEsigma.Rd | 1 man/plot.ADMM.Rd | 1 man/plot.RIDGE.Rd | 1 src/CV.cpp | 20 +++++--- src/CVP.cpp | 14 +++-- src/RcppExports.cpp | 8 +-- src/Sigma.cpp | 20 ++++---- src/Sigma.h | 2 vignettes |only 23 files changed, 324 insertions(+), 172 deletions(-)
Title: Convert Rd to 'Roxygen' Documentation
Description: Functions to convert Rd to 'roxygen' documentation. It can parse an
Rd file to a list, create the 'roxygen' documentation and update the original
R script (e.g. the one containing the definition of the function)
accordingly. This package also provides utilities that can help developers
build packages using 'roxygen' more easily. The 'formatR' package can be used
to reformat the R code in the examples sections so that the code will be
more readable.
Author: Hadley Wickham [aut],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between Rd2roxygen versions 1.6.2 dated 2017-03-30 and 1.7 dated 2018-08-02
DESCRIPTION | 12 - MD5 | 20 +- NAMESPACE | 1 NEWS | 6 R/build.R | 12 - build/vignette.rds |binary inst/doc/Rd2roxygen.R | 19 + inst/doc/Rd2roxygen.Rmd | 13 - inst/doc/Rd2roxygen.html | 401 +++++++++++++++++++++++++++++++++-------- inst/examples/parse_and_save.R | 18 - vignettes/Rd2roxygen.Rmd | 13 - 11 files changed, 387 insertions(+), 128 deletions(-)
Title: Differential Item Functioning in Generalized Partial Credit
Models
Description: Provides a function to detect Differential Item Functioning (DIF) in Generalized Partial Credit Models (GPCM) and special cases of the GPCM. A joint model is set up where DIF is explicitly parametrized and penalized likelihood estimation is used for parameter selection. The big advantage of the method called GPCMlasso is that several variables can be treated simultaneously and that both continuous and categorical variables can be used to detect DIF.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther@stat.uni-muenchen.de>
Diff between GPCMlasso versions 0.1-1 dated 2018-02-12 and 0.1-2 dated 2018-08-02
DESCRIPTION | 12 +++++----- MD5 | 42 +++++++++++++++++------------------ R/GPCMlasso-package.R | 3 -- R/GPCMlasso.R | 16 +++++++------ R/ctrl_GPCMlasso.R | 3 -- R/design_GPCMlasso.R | 16 +++++++++++-- R/fit_GPCMlasso.R | 5 ++-- R/get_designX.R | 43 +++++++++++++++++++++++++++++++++++- R/help_fit.R | 8 +++++- R/person.posterior.R | 3 -- R/plot.GPCMlasso.R | 16 ++++++++----- R/predict.GPCMlasso.R | 3 -- R/print.GPCMlasso.R | 30 +++++++++++++++++-------- R/sim_fun.R | 1 man/GPCMlasso-package.Rd | 3 -- man/GPCMlasso.Rd | 9 +++++-- man/ctrl_GPCMlasso.Rd | 3 -- man/plot.GPCMlasso.Rd | 3 -- man/predict.GPCMlasso.Rd | 3 -- man/print.GPCMlasso.Rd | 3 -- man/trait.posterior.Rd | 3 -- src/cppGPCMlasso.cpp | 55 +++++++++++++++++++++++++++++++++++++++-------- 22 files changed, 193 insertions(+), 90 deletions(-)
Title: Tools for Making and Combining Functions
Description: Provides a suite of function-building tools centered around a
(forward) composition operator, %>>>%, which extends the semantics of the
'magrittr' %>% operator and supports 'tidyverse' quasiquotation. It enables
you to construct composite functions that can be inspected and transformed as
list-like objects. In conjunction with %>>>%, a compact function constructor,
fn(), and a function that performs partial application, partial(), are also
provided. Both support quasiquotation.
Author: Eugene Ha [aut, cre]
Maintainer: Eugene Ha <eha@posteo.de>
Diff between gestalt versions 0.1.2 dated 2018-07-09 and 0.1.4 dated 2018-08-02
DESCRIPTION | 10 +++++----- MD5 | 20 +++++++++++++------- NAMESPACE | 5 +++++ R/compose.R | 36 ++++++++++++++++++++++-------------- R/context.R |only R/fn.R | 9 +++++---- R/posure.R |only man/compose.Rd | 13 +++++++++---- man/context.Rd |only man/posure.Rd |only tests/testthat/test-compose.R | 39 ++++++++++++++++++++++++++++++++++++++- tests/testthat/test-context.R |only tests/testthat/test-posure.R |only tests/testthat/test-print.R | 39 +++++++++++++++++++++++++++++++++++++++ 14 files changed, 136 insertions(+), 35 deletions(-)
Title: Cross-Validated (Nested) Forward Selection
Description: Implementation of forward selection based on cross-validated
linear and logistic regression.
Author: Marco Colombo [aut, cre] (<https://orcid.org/0000-0001-6672-0623>),
Felix Agakov [ctb]
Maintainer: Marco Colombo <m.colombo@ed.ac.uk>
Diff between nestfs versions 0.8.4 dated 2018-07-05 and 0.8.5 dated 2018-08-02
DESCRIPTION | 8 - MD5 | 8 - R/nestfs.R | 237 +++++++++++++++++++++++++++++++---------------- man/forward.selection.Rd | 6 - man/nested.glm.Rd | 14 +- 5 files changed, 177 insertions(+), 96 deletions(-)
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 2.2.4 dated 2018-06-02 and 2.2.5 dated 2018-08-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/gjamHfunctions.R | 12 +++++++----- inst/doc/gjamVignette.Rmd | 2 +- inst/doc/gjamVignette.html | 30 +++++++++++++++--------------- man/gjam-package.Rd | 4 ++-- vignettes/gjamVignette.Rmd | 2 +- 7 files changed, 36 insertions(+), 34 deletions(-)
Title: Lighten your R Model Outputs
Description: The strip function deletes components of R model outputs that are useless for specific purposes, such as predict[ing], print[ing], summary[izing], etc.
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>
Diff between strip versions 0.1.1 dated 2017-01-12 and 0.1.7 dated 2018-08-02
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++----------- NAMESPACE | 2 ++ NEWS.md | 17 +++++++++++++++++ R/strip.default.R | 3 ++- R/strip.gam.R | 4 +++- R/strip.glm.R | 4 +++- R/strip.kmeans.R |only R/strip.lm.R | 18 +++++++++++++++++- R/strip.randomForest.R | 4 +++- R/strip.train.R | 4 +++- README.md | 2 +- man/strip.Rd | 22 +++++++++++++--------- 13 files changed, 81 insertions(+), 32 deletions(-)
Title: Detect Heatwaves and Cold-Spells
Description: The different methods of defining and detecting extreme events, known as heatwaves or cold-spells in both air and water temperature data are encompassed within this package. These detection algorithms may be used on non-temperature data as well however, this is not catered for explicitly here as no use of this technique in the literature currently exists.
Author: Robert W. Schlegel [aut, cre, ctb]
(<https://orcid.org/0000-0002-0705-1287>),
Albertus J. Smit [aut, ctb] (<https://orcid.org/0000-0002-3799-6126>)
Maintainer: Robert W. Schlegel <robwschlegel@gmail.com>
Diff between heatwaveR versions 0.3.0 dated 2018-06-22 and 0.3.3 dated 2018-08-02
heatwaveR-0.3.0/heatwaveR/vignettes/fig-example-10-1.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example-11-1.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example1-1.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example2-1.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example3-1.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example3-2.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example4-1.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example5-1.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example6-1.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example6-2.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example7-1.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example7-2.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example8-1.png |only heatwaveR-0.3.0/heatwaveR/vignettes/fig-example9-1.png |only heatwaveR-0.3.3/heatwaveR/DESCRIPTION | 10 heatwaveR-0.3.3/heatwaveR/MD5 | 76 +- heatwaveR-0.3.3/heatwaveR/NEWS.md | 26 heatwaveR-0.3.3/heatwaveR/R/clim_spread.R | 20 heatwaveR-0.3.3/heatwaveR/R/detect_event.R | 16 heatwaveR-0.3.3/heatwaveR/R/exceedance.R | 34 heatwaveR-0.3.3/heatwaveR/R/make_whole_fast.R | 25 heatwaveR-0.3.3/heatwaveR/R/na_interp.R | 1 heatwaveR-0.3.3/heatwaveR/R/smooth_percentile.R | 1 heatwaveR-0.3.3/heatwaveR/R/ts2clm.R | 20 heatwaveR-0.3.3/heatwaveR/README.md | 352 ---------- heatwaveR-0.3.3/heatwaveR/build/vignette.rds |binary heatwaveR-0.3.3/heatwaveR/inst/doc/OISST_preparation.html | 4 heatwaveR-0.3.3/heatwaveR/inst/doc/complex_clims.R | 30 heatwaveR-0.3.3/heatwaveR/inst/doc/complex_clims.Rmd | 75 +- heatwaveR-0.3.3/heatwaveR/inst/doc/complex_clims.html | 75 +- heatwaveR-0.3.3/heatwaveR/inst/doc/detection_and_visualisation.R |only heatwaveR-0.3.3/heatwaveR/inst/doc/detection_and_visualisation.Rmd |only heatwaveR-0.3.3/heatwaveR/inst/doc/detection_and_visualisation.html |only heatwaveR-0.3.3/heatwaveR/inst/doc/event_categories.R |only heatwaveR-0.3.3/heatwaveR/inst/doc/event_categories.Rmd |only heatwaveR-0.3.3/heatwaveR/inst/doc/event_categories.html |only heatwaveR-0.3.3/heatwaveR/inst/doc/exceedance.R |only heatwaveR-0.3.3/heatwaveR/inst/doc/exceedance.Rmd |only heatwaveR-0.3.3/heatwaveR/inst/doc/exceedance.html |only heatwaveR-0.3.3/heatwaveR/inst/doc/gridded_event_detection.Rmd | 1 heatwaveR-0.3.3/heatwaveR/inst/doc/gridded_event_detection.html | 4 heatwaveR-0.3.3/heatwaveR/man/detect_event.Rd | 16 heatwaveR-0.3.3/heatwaveR/man/exceedance.Rd | 7 heatwaveR-0.3.3/heatwaveR/src/clim_calc.cpp | 8 heatwaveR-0.3.3/heatwaveR/tests/testthat/test-clim_spread.R | 11 heatwaveR-0.3.3/heatwaveR/tests/testthat/test-ts2clm.R | 10 heatwaveR-0.3.3/heatwaveR/vignettes/bibliography.bib | 1 heatwaveR-0.3.3/heatwaveR/vignettes/complex_clims.Rmd | 75 +- heatwaveR-0.3.3/heatwaveR/vignettes/detection_and_visualisation.Rmd |only heatwaveR-0.3.3/heatwaveR/vignettes/event_categories.Rmd |only heatwaveR-0.3.3/heatwaveR/vignettes/exceedance.Rmd |only heatwaveR-0.3.3/heatwaveR/vignettes/gridded_event_detection.Rmd | 1 52 files changed, 438 insertions(+), 461 deletions(-)
Title: Segmentation and Classification of Accelerometer Data
Description: Segmentation and classification procedures for data from the 'Activinsights GENEActiv' <https://www.activinsights.com/products/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing.
Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.
Author: Chris Campbell [aut],
Aimee Gott [aut],
Joss Langford [aut],
Charles Sweetland [aut, cre],
Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@sweetland-solutions.co.uk>
Diff between GENEAclassify versions 1.4.12 dated 2018-07-07 and 1.4.13 dated 2018-08-02
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/classifyGENEA.R | 3 +++ R/dataImport.R | 6 +++--- R/getGENEAsegments.R | 4 +++- build/vignette.rds |binary man/classifyGENEA.Rd | 4 +++- man/dataImport.Rd | 5 ++++- man/getGENEAsegments.Rd | 11 +++++++---- 9 files changed, 35 insertions(+), 22 deletions(-)
Title: Convex Hull
Description: Computes the convex hull in arbitrary dimension, based on the Qhull library (<http://www.qhull.org>). The package provides a complete description of the convex hull: edges, ridges, facets, adjacencies. Triangulation is optional.
Author: C. B. Barber [cph] (author of the Qhull library),
The Geometry Center [cph],
Stéphane Laurent [cph, aut, cre]
Maintainer: Stéphane Laurent <laurent_step@yahoo.fr>
Diff between cxhull versions 0.1.0 dated 2018-07-31 and 0.1.1 dated 2018-08-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ inst/doc/truncated_tesseract.html | 16 ++++++++-------- src/convexhull.c | 17 ++++++++++++----- 5 files changed, 33 insertions(+), 21 deletions(-)
Title: Makefile Generator for R Analytical Projects
Description: Creates and maintains a build process for complex analytic tasks in R.
Package allows to easily generate Makefile for the (GNU) 'make' tool, which drives the build process
by (in parallel) executing build commands in order to update results accordingly to given dependencies
on changed data or updated source files.
Author: Michal Burda
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between rmake versions 1.0.0 dated 2018-03-22 and 1.0.1 dated 2018-08-02
DESCRIPTION | 10 +++---- MD5 | 43 ++++++++++++++++-------------- NAMESPACE | 1 R/getParam.R |only R/inShell.R | 9 +++++- R/makefile.R | 52 +++++++++++++++++++++++++++++-------- R/markdownRule.R | 18 ++++++++++-- R/offlineRule.R | 2 - R/rRule.R | 16 +++++++++-- R/rmake.R | 2 - R/rmakeSkeleton.R | 4 ++ man/defaultVars.Rd | 2 - man/getParam.Rd |only man/markdownRule.Rd | 9 ++++-- man/offlineRule.Rd | 2 - man/rRule.Rd | 8 ++++- man/rmake-package.Rd | 2 - man/rule.Rd | 4 +- tests/testthat/test-getParam.R |only tests/testthat/test-makefile.R | 38 +++++++++++++++++++-------- tests/testthat/test-markdownRule.R | 8 ++++- tests/testthat/test-rRule.R | 8 ++++- tests/testthat/test-run-simple.R | 3 ++ tests/testthat/test-run-tasks.R | 3 ++ 24 files changed, 175 insertions(+), 69 deletions(-)
Title: Multivariate Multiscale Framework for Independence Tests
Description: Test for independence of two random vectors, learn and report the dependency structure. For more information, see Gorsky and Ma (2018) <arXiv:1806.06777>.
Author: S. Gorsky, L. Ma
Maintainer: S. Gorsky <s.gorsky@duke.edu>
Diff between MultiFit versions 0.1.0 dated 2018-07-31 and 0.1.1 dated 2018-08-02
DESCRIPTION | 6 - MD5 | 17 ++--- NEWS.md |only inst/doc/multiFit.R | 18 ++--- inst/doc/multiFit.Rmd | 22 +++--- inst/doc/multiFit.html | 157 ++++++++++++++++++++++--------------------------- src/discretize.cpp | 2 src/makeCDF.cpp | 6 - src/singleFisher.cpp | 7 -- vignettes/multiFit.Rmd | 22 +++--- 10 files changed, 121 insertions(+), 136 deletions(-)
Title: Read Hierarchical Fixed Width Files
Description: Read hierarchical fixed width files like those commonly used by
many census data providers. Also allows for reading of data in chunks,
and reading 'gzipped' files without storing the full file in memory.
Author: Greg Freedman Ellis [aut, cre],
Derek Burk [ctb],
Joe Grover [ctb],
Mark Padgham [ctb],
Hadley Wickham [ctb] (Code adapted from readr),
Jim Hester [ctb] (Code adapted from readr),
Romain Francois [ctb] (Code adapted from readr),
R Core Team [ctb] (Code adapted from readr),
RStudio [cph, fnd] (Code adapted from readr),
Jukka Jylänki [ctb, cph] (Code adapted from readr),
Mikkel Jørgensen [ctb, cph] (Code adapted from readr),
University of Minnesota [cph]
Maintainer: Greg Freedman Ellis <gfellis@umn.edu>
Diff between hipread versions 0.1.0 dated 2018-07-30 and 0.1.1 dated 2018-08-02
DESCRIPTION | 10 ++-- MD5 | 23 +++++----- NAMESPACE | 1 NEWS.md |only R/arg_checkers.R | 75 +++++++++++++++++----------------- R/callbacks.R | 13 +++-- R/col_specs.R | 2 R/hipread.R |only man/hipread-package.Rd |only src/column.cpp | 3 - src/gzstream.cpp | 2 src/gzstream.h | 2 tests/testthat/test-callback-compat.R | 2 tests/testthat/test-long-chunk.R | 4 + 14 files changed, 76 insertions(+), 61 deletions(-)
Title: Distributed Lag Non-Linear Models
Description: Collection of functions for distributed lag linear and non-linear models.
Author: Antonio Gasparrini [aut, cre],
Ben Armstrong [aut],
Fabian Scheipl [ctb]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between dlnm versions 2.3.4 dated 2017-12-06 and 2.3.5 dated 2018-08-02
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- NEWS.md | 10 ++++++++++ R/getlink.R | 5 +++-- build/vignette.rds |binary inst/CITATION | 35 ++++++++++++++++++----------------- inst/NEWS | 10 ++++++++++ inst/doc/dlnmExtended.pdf |binary inst/doc/dlnmOverview.pdf |binary inst/doc/dlnmPenalized.pdf |binary inst/doc/dlnmTS.pdf |binary man/crosspred.Rd | 2 +- 13 files changed, 60 insertions(+), 38 deletions(-)
Title: Unified Interface to Distance, Dissimilarity, Similarity
Matrices
Description: Provides a high level API to interface over sources storing distance, dissimilarity, similarity matrices with matrix style extraction, replacement and other utilities. Currently, in-memory dist object backend is supported.
Author: KS Srikanth [aut, cre]
Maintainer: KS Srikanth <sri.teach@gmail.com>
Diff between disto versions 0.1.0 dated 2018-07-19 and 0.2.0 dated 2018-08-02
disto-0.1.0/disto/inst/doc/vignette_disto.html |only disto-0.1.0/disto/man/distExtractPair.Rd |only disto-0.2.0/disto/DESCRIPTION | 7 disto-0.2.0/disto/MD5 | 20 - disto-0.2.0/disto/NEWS.md |only disto-0.2.0/disto/R/dist_extractors.R | 424 ++++++++++++------------- disto-0.2.0/disto/R/disto_methods.R | 38 +- disto-0.2.0/disto/build/vignette.rds |binary disto-0.2.0/disto/inst/doc/vignette_disto.R | 16 disto-0.2.0/disto/inst/doc/vignette_disto.Rmd | 31 + disto-0.2.0/disto/inst/doc/vignette_disto.pdf |only disto-0.2.0/disto/man/dapply.Rd | 6 disto-0.2.0/disto/vignettes/vignette_disto.Rmd | 31 + 13 files changed, 298 insertions(+), 275 deletions(-)
More information about cromwellDashboard at CRAN
Permanent link
Title: Plotting for Bayesian Models
Description: Plotting functions for posterior analysis, model checking,
and MCMC diagnostics. The package is designed not only to provide convenient
functionality for users, but also a common set of functions that can be
easily used by developers working on a variety of R packages for Bayesian
modeling, particularly (but not exclusively) packages interfacing with 'Stan'.
Author: Jonah Gabry [aut, cre],
Tristan Mahr [aut],
Paul-Christian Bürkner [ctb],
Martin Modrák [ctb],
Malcolm Barrett [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between bayesplot versions 1.5.0 dated 2018-03-30 and 1.6.0 dated 2018-08-02
DESCRIPTION | 26 - MD5 | 131 +++-- NAMESPACE | 5 NEWS.md | 45 +- R/bayesplot-ggplot-themes.R | 151 +++++- R/bayesplot_grid.R | 15 R/helpers-gg.R | 2 R/helpers-shared.R | 48 +- R/mcmc-combo.R | 2 R/mcmc-diagnostics-nuts.R | 33 + R/mcmc-diagnostics.R | 44 +- R/mcmc-distributions.R | 15 R/mcmc-intervals.R | 3 R/mcmc-overview.R | 10 R/mcmc-parcoord.R | 6 R/mcmc-recover.R | 13 R/mcmc-scatterplots.R | 27 - R/mcmc-traces.R | 3 R/ppc-discrete.R | 16 R/ppc-distributions.R | 95 ++-- R/ppc-errors.R | 13 R/ppc-intervals.R | 78 ++- R/ppc-loo.R | 170 ++++--- R/ppc-scatterplots.R | 6 R/ppc-test-statistics.R | 16 R/zzz.R | 7 build/vignette.rds |binary inst/doc/graphical-ppcs.R | 6 inst/doc/graphical-ppcs.Rmd | 2 inst/doc/graphical-ppcs.html | 47 +- inst/doc/plotting-mcmc-draws.R | 6 inst/doc/plotting-mcmc-draws.Rmd | 2 inst/doc/plotting-mcmc-draws.html | 43 + inst/doc/visual-mcmc-diagnostics.R | 192 ++++++-- inst/doc/visual-mcmc-diagnostics.Rmd | 701 ++++++++++++++++++++------------ inst/doc/visual-mcmc-diagnostics.html | 380 +++++++++-------- man/MCMC-diagnostics.Rd | 13 man/MCMC-distributions.Rd | 45 +- man/MCMC-intervals.Rd | 38 - man/MCMC-nuts.Rd | 2 man/MCMC-overview.Rd | 10 man/MCMC-parcoord.Rd | 42 + man/MCMC-recover.Rd | 10 man/MCMC-scatterplots.Rd | 49 +- man/MCMC-traces.Rd | 36 - man/PPC-discrete.Rd | 10 man/PPC-distributions.Rd | 23 - man/PPC-errors.Rd | 12 man/PPC-intervals.Rd | 28 - man/PPC-loo.Rd | 61 +- man/PPC-test-statistics.Rd | 12 man/bayesplot_grid.Rd | 8 man/bayesplot_theme_get.Rd |only man/figures/stanlogo.png |binary man/theme_default.Rd | 32 - tests/testthat/Rplots.pdf |binary tests/testthat/test-aesthetics.R | 54 ++ tests/testthat/test-helpers-shared.R | 6 tests/testthat/test-mcmc-diagnostics.R | 2 tests/testthat/test-mcmc-intervals.R | 34 - tests/testthat/test-ppc-distributions.R | 6 tests/testthat/test-ppc-intervals.R | 37 + tests/testthat/test-ppc-loo.R | 69 +-- vignettes/children/SETTINGS-knitr.txt | 3 vignettes/graphical-ppcs.Rmd | 2 vignettes/plotting-mcmc-draws.Rmd | 2 vignettes/visual-mcmc-diagnostics.Rmd | 701 ++++++++++++++++++++------------ 67 files changed, 2381 insertions(+), 1325 deletions(-)
Title: Play with the Tribe of Attributes
Description: Functions to make manipulation of object attributes easier.
It also contains a few functions that extend the 'dplyr' package for data
manipulation, and it provides new pipe operators, including the pipe '%@>%'
similar to the 'magrittr' '%>%', but with the additional functionality to
enable attributes propagation.
Author: Paul Poncet [aut, cre],
Stefan Milton Bache [aut] (for functions copied or modified from the
'magrittr' package),
Hadley Wickham [aut] (for functions copied or modified from the
'magrittr' package)
Maintainer: Paul Poncet <paulponcet@yahoo.fr>
Diff between tribe versions 0.1.6 dated 2017-11-14 and 0.1.7 dated 2018-08-02
tribe-0.1.6/tribe/man/define.Rd |only tribe-0.1.7/tribe/DESCRIPTION | 8 tribe-0.1.7/tribe/MD5 | 40 +- tribe-0.1.7/tribe/NAMESPACE | 8 tribe-0.1.7/tribe/NEWS.md | 8 tribe-0.1.7/tribe/R/at.R | 14 tribe-0.1.7/tribe/R/pipe.R | 6 tribe-0.1.7/tribe/R/shield.R | 6 tribe-0.1.7/tribe/R/stick_to.R | 6 tribe-0.1.7/tribe/R/tribe.R | 2 tribe-0.1.7/tribe/R/verbs_for_attributes.R | 109 +----- tribe-0.1.7/tribe/README.md | 32 - tribe-0.1.7/tribe/build/vignette.rds |binary tribe-0.1.7/tribe/inst/doc/tribe-vignette.R | 18 - tribe-0.1.7/tribe/inst/doc/tribe-vignette.Rmd | 32 - tribe-0.1.7/tribe/inst/doc/tribe-vignette.html | 442 ++++++++++++++++++------- tribe-0.1.7/tribe/man/at.Rd | 3 tribe-0.1.7/tribe/man/at_mutate.Rd |only tribe-0.1.7/tribe/man/make_pipe.Rd | 6 tribe-0.1.7/tribe/man/shield.Rd | 6 tribe-0.1.7/tribe/man/tribe.Rd | 2 tribe-0.1.7/tribe/vignettes/tribe-vignette.Rmd | 32 - 22 files changed, 483 insertions(+), 297 deletions(-)
Title: 'Rcpp' Implementation of 'FSelector' Entropy-Based Feature
Selection Algorithms with a Sparse Matrix Support
Description: 'Rcpp' (free of 'Java'/'Weka') implementation of 'FSelector' entropy-based feature selection
algorithms based on an MDL discretization (Fayyad U. M., Irani K. B.: Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning.
In 13'th International Joint Conference on Uncertainly in Artificial Intelligence (IJCAI93), pages 1022-1029, Chambery, France, 1993.) <https://www.ijcai.org/Proceedings/93-2/Papers/022.pdf>
with a sparse matrix support. It is also equipped with a parallel backend.
Author: Zygmunt Zawadzki [aut, cre],
Marcin Kosinski [aut],
Krzysztof Slomczynski [ctb],
Damian Skrzypiec [ctb]
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>
Diff between FSelectorRcpp versions 0.1.10 dated 2018-06-27 and 0.2.1 dated 2018-08-02
FSelectorRcpp-0.1.10/FSelectorRcpp/inst/test.R |only FSelectorRcpp-0.2.1/FSelectorRcpp/DESCRIPTION | 11 FSelectorRcpp-0.2.1/FSelectorRcpp/MD5 | 46 FSelectorRcpp-0.2.1/FSelectorRcpp/NAMESPACE | 6 FSelectorRcpp-0.2.1/FSelectorRcpp/R/discretize.R | 108 + FSelectorRcpp-0.2.1/FSelectorRcpp/R/discretize_transform.R |only FSelectorRcpp-0.2.1/FSelectorRcpp/R/feature_search.R | 8 FSelectorRcpp-0.2.1/FSelectorRcpp/R/utils.R | 1 FSelectorRcpp-0.2.1/FSelectorRcpp/build/vignette.rds |binary FSelectorRcpp-0.2.1/FSelectorRcpp/inst/doc/benchmarks_discretize.R | 4 FSelectorRcpp-0.2.1/FSelectorRcpp/inst/doc/benchmarks_discretize.Rmd | 4 FSelectorRcpp-0.2.1/FSelectorRcpp/inst/doc/benchmarks_discretize.html | 719 +++++++++- FSelectorRcpp-0.2.1/FSelectorRcpp/inst/doc/get_started.html | 715 +++++++++ FSelectorRcpp-0.2.1/FSelectorRcpp/inst/include/discretize/discretizeControl.h | 7 FSelectorRcpp-0.2.1/FSelectorRcpp/man/discretize.Rd | 28 FSelectorRcpp-0.2.1/FSelectorRcpp/man/discretize_transform.Rd |only FSelectorRcpp-0.2.1/FSelectorRcpp/man/feature_search.Rd | 1 FSelectorRcpp-0.2.1/FSelectorRcpp/man/to_formula.Rd | 1 FSelectorRcpp-0.2.1/FSelectorRcpp/src/discretize.cpp | 3 FSelectorRcpp-0.2.1/FSelectorRcpp/tests/testthat/test-cutoff.R | 26 FSelectorRcpp-0.2.1/FSelectorRcpp/tests/testthat/test-discretize.R | 100 - FSelectorRcpp-0.2.1/FSelectorRcpp/tests/testthat/test-discretize_transform.R |only FSelectorRcpp-0.2.1/FSelectorRcpp/tests/testthat/test-information_gain.R | 79 - FSelectorRcpp-0.2.1/FSelectorRcpp/tests/testthat/test-param-search.R | 57 FSelectorRcpp-0.2.1/FSelectorRcpp/tests/testthat/test-support.R | 27 FSelectorRcpp-0.2.1/FSelectorRcpp/vignettes/benchmarks_discretize.Rmd | 4 26 files changed, 1762 insertions(+), 193 deletions(-)
Title: An Easy Way to Report ROC Analysis
Description: Provides an easy way to report the results of ROC analysis, including:
1. an ROC curve. 2. the value of Cutoff, AUC (Area Under Curve), ACC (accuracy),
SEN (sensitivity), SPE (specificity),
PLR (positive likelihood ratio), NLR (negative likelihood ratio),
PPV (positive predictive value), NPV (negative predictive value).
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between reportROC versions 3.0 dated 2017-10-30 and 3.1 dated 2018-08-02
DESCRIPTION | 15 +- MD5 | 6 R/reportROC.R | 337 ++++++++++++++++++++++++++++++------------------------- man/reportROC.Rd | 15 +- 4 files changed, 204 insertions(+), 169 deletions(-)
Title: LncRNA Identification and Analysis Using Heterologous Features
Description: Long non-coding RNAs identification and analysis. Default models are trained with human, mouse and wheat datasets by employing SVM. Features are based on intrinsic composition of sequence, EIIP value (electron-ion interaction pseudopotential), and secondary structure. This package can also extract other classic features and build new classifiers. Reference: Han SY., Liang YC., Li Y., et al. (2018) <doi:10.1093/bib/bby065>.
Author: Siyu HAN [aut, cre],
Ying LI [aut],
Yanchun LIANG [aut]
Maintainer: Siyu HAN <hansy15@mails.jlu.edu.cn>
Diff between LncFinder versions 1.0.0 dated 2017-02-06 and 1.1.3 dated 2018-08-02
LncFinder-1.0.0/LncFinder/man/max_orf.Rd |only LncFinder-1.1.3/LncFinder/DESCRIPTION | 40 LncFinder-1.1.3/LncFinder/MD5 | 42 LncFinder-1.1.3/LncFinder/NAMESPACE | 19 LncFinder-1.1.3/LncFinder/NEWS.md |only LncFinder-1.1.3/LncFinder/R/LncFinder.R | 2280 +++++++++++++++--- LncFinder-1.1.3/LncFinder/R/data.R | 18 LncFinder-1.1.3/LncFinder/README.md |only LncFinder-1.1.3/LncFinder/inst |only LncFinder-1.1.3/LncFinder/man/build_model.Rd | 20 LncFinder-1.1.3/LncFinder/man/compute_EIIP.Rd |only LncFinder-1.1.3/LncFinder/man/compute_EucDistance.Rd |only LncFinder-1.1.3/LncFinder/man/compute_FickettScore.Rd |only LncFinder-1.1.3/LncFinder/man/compute_GC.Rd |only LncFinder-1.1.3/LncFinder/man/compute_LogDistance.Rd |only LncFinder-1.1.3/LncFinder/man/compute_hexamerScore.Rd |only LncFinder-1.1.3/LncFinder/man/compute_kmer.Rd |only LncFinder-1.1.3/LncFinder/man/compute_pI.Rd |only LncFinder-1.1.3/LncFinder/man/demo_DNA.seq.Rd | 4 LncFinder-1.1.3/LncFinder/man/demo_SS.seq.Rd | 8 LncFinder-1.1.3/LncFinder/man/demo_dataset.Rd | 6 LncFinder-1.1.3/LncFinder/man/extract_features.Rd | 36 LncFinder-1.1.3/LncFinder/man/find_orfs.Rd |only LncFinder-1.1.3/LncFinder/man/lnc_finder.Rd | 34 LncFinder-1.1.3/LncFinder/man/make_frequencies.Rd | 48 LncFinder-1.1.3/LncFinder/man/make_referFreq.Rd |only LncFinder-1.1.3/LncFinder/man/read_SS.Rd |only LncFinder-1.1.3/LncFinder/man/run_RNAfold.Rd | 14 LncFinder-1.1.3/LncFinder/man/svm_cv.Rd |only LncFinder-1.1.3/LncFinder/man/svm_tune.Rd | 28 30 files changed, 2143 insertions(+), 454 deletions(-)
Title: Fits a Principal Curve in Arbitrary Dimension
Description: Fitting a principal curve to a data matrix in arbitrary dimensions.
Author: Trevor Hastie [aut],
Andreas Weingessel [aut],
Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>),
Henrik Bengtsson [ctb] (HenrikBengtsson),
Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between princurve versions 2.1.2 dated 2018-07-24 and 2.1.2.1 dated 2018-08-02
DESCRIPTION | 6 MD5 | 16 R/get.lam.R | 8 R/principal.curve.R | 10 build/vignette.rds |binary inst/doc/intro.html | 1281 ++++++++++++++++++++++++++++++++- tests/testthat/test-legacy_princurve.R | 36 tests/testthat/test-principal_curve.R | 12 tests/testthat/test-project_to_curve.R | 12 9 files changed, 1317 insertions(+), 64 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-08 0.0.25
2013-03-08 0.0.23
2011-10-09 0.0.21
2011-10-01 0.0.20