Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Gur Yaari [aut],
Namita Gupta [aut],
Jason Vander Heiden [aut, cre],
Ang Cui [ctb],
Susanna Marquez [ctb],
Julian Zhou [ctb],
Nima Nouri [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between shazam versions 0.2.0 dated 2019-07-18 and 0.2.1 dated 2019-07-19
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 9 +++++++++ R/DistToNearest.R | 19 +++++++++++++------ inst/doc/Baseline-Vignette.pdf |binary inst/doc/DistToNearest-Vignette.pdf |binary inst/doc/Mutation-Vignette.pdf |binary inst/doc/Shmulate-Vignette.pdf |binary inst/doc/Targeting-Vignette.pdf |binary 9 files changed, 34 insertions(+), 18 deletions(-)
Title: Look Up Time Zones of Point Coordinates
Description: Input latitude and longitude values or an 'sf/sfc' POINT
object and get back the time zone in which they exist. Two methods are implemented.
One is very fast and uses 'Rcpp' in conjunction with data from the 'Javascript' library
(<https://github.com/darkskyapp/tz-lookup/>). This method also works outside of countries'
borders and in international waters, however speed comes at the cost of accuracy - near time
zone borders away from populated centres there is a chance that it will return the incorrect
time zone. The other method is slower but more accurate - it uses the 'sf' package to intersect
points with a detailed map of time zones from here:
<https://github.com/evansiroky/timezone-boundary-builder/>. The package also
contains several utility functions for helping to understand and visualize
time zones, such as listing of world time zones, including information about
daylight savings times and their offsets from UTC. You can also plot a
time zone to visualize the UTC offset over a year and when daylight savings
times are in effect.
Author: Andy Teucher [aut, cre] (<https://orcid.org/0000-0002-7840-692X>),
Bob Rudis [ctb] (<https://orcid.org/0000-0001-5670-2640>)
Maintainer: Andy Teucher <andy.teucher@gmail.com>
Diff between lutz versions 0.3.0 dated 2019-07-14 and 0.3.1 dated 2019-07-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/olson.R | 23 +++++++++++++++-------- R/utils.R | 2 ++ tests/testthat/test-olson.R | 4 ++++ 6 files changed, 33 insertions(+), 16 deletions(-)
Title: Analysis Of The Interpopulation Difference In Degree of Sexual
Dimorphism Using Summary Statistics
Description: Provides two approaches of comparison; the univariate and the multivariate analysis in two or more populations. Since the main obstacle of performing systematic comparisons in anthropological studies is the absence of raw data, the current package offer a solution for this problem by allowing the use of published summary statistics of metric data (mean, standard deviation and sex specific sample size) as illustrated by the works of Greene, D. L. (1989) <doi:10.1002/ajpa.1330790113> and Konigsberg, L. W. (1991) <doi:10.1002/ajpa.1330840110>.
Author: Bassam A. Abulnoor [aut, cre] (<https://orcid.org/0000-0003-4351-2754>),
MennattAllah H. Attia [aut] (<https://orcid.org/0000-0002-2304-532X>),
Lyle W. Konigsberg [ctb, dtc] (<https://orcid.org/0000-0003-4052-1575>)
Maintainer: Bassam A. Abulnoor <bas12@fayoum.edu.eg>
Diff between TestDimorph versions 0.1.0 dated 2019-06-14 and 0.2.0 dated 2019-07-19
DESCRIPTION | 61 +++++++++++++++------------------ MD5 | 44 +++++++++++++----------- NAMESPACE | 27 ++++++++++++++ NEWS.md |only R/AccuModel.R |only R/RawGen.R |only R/Tg.R | 32 +++++++++-------- R/aovSS.R | 8 ++-- R/data.R | 4 +- R/extract_sum.R | 86 ++++++++++++++++++++++++----------------------- R/multivariate.R | 17 +++++---- R/pMatrix.R | 41 ++++++++++++++-------- R/univariate.R | 12 +++--- README.md |only build/partial.rdb |binary inst/REFERENCES.bib | 9 ++++ man/AccuModel.Rd |only man/RawGen.Rd |only man/Tg.Rd | 5 +- man/aovSS.Rd | 7 ++- man/baboon.parms_df.Rd | 2 - man/baboon.parms_list.Rd | 2 - man/extract_sum.Rd | 29 +++++++++------ man/multivariate.Rd | 16 ++++---- man/pMatrix.Rd | 35 ++++++++++--------- man/univariate.Rd | 11 +++--- 26 files changed, 261 insertions(+), 187 deletions(-)
Title: Forecasting Long-Term Growth of the U.S. Stock Market and
Business Cycles
Description: A long-term forecast model called "Jubilee-Tectonic model" is implemented to forecast future returns of the U.S. stock market, Treasury yield, and gold price. The five-factor model forecasts the 10-year and 20-year future equity returns with high R-squared above 80 percent. It is based on linear growth and mean reversion characteristics in the U.S. stock market. This model also enhances the CAPE model by introducing the hypothesis that there are fault lines in the historical CAPE, which can be calibrated and corrected through statistical learning. In addition, it contains a module for business cycles, optimal interest rate, and recession forecasts.
Author: Stephen H-T. Lihn [aut, cre]
Maintainer: Stephen H-T. Lihn <stevelihn@gmail.com>
Diff between jubilee versions 0.2.5 dated 2018-09-11 and 0.3.1 dated 2019-07-19
jubilee-0.2.5/jubilee/inst/doc/important-dates-in-us-history-chart.pdf |only jubilee-0.2.5/jubilee/inst/doc/jubilee-manual.pdf |only jubilee-0.2.5/jubilee/vignettes/z-jubi-tut-20y-smr-GSI-plot-1.tikz |only jubilee-0.2.5/jubilee/vignettes/z-jubi-tut-20y-smr-YS-plot-1.tikz |only jubilee-0.2.5/jubilee/vignettes/z-jubi-tut-20y-smr-raw-plot-1.tikz |only jubilee-0.2.5/jubilee/vignettes/z-jubi-tut-demo-Yt-1.tikz |only jubilee-0.2.5/jubilee/vignettes/z-jubi-tut-forecast-10y-X-1.tikz |only jubilee-0.2.5/jubilee/vignettes/z-jubi-tut-forecast-10y-rtn-1.tikz |only jubilee-0.2.5/jubilee/vignettes/z-jubi-tut-forecast-20y-X-1.tikz |only jubilee-0.2.5/jubilee/vignettes/z-jubi-tut-forecast-20y-rtn-1.tikz |only jubilee-0.2.5/jubilee/vignettes/z-jubi-tut-inflation-1.tikz |only jubilee-0.2.5/jubilee/vignettes/z-jubi-tut-unrate-1.tikz |only jubilee-0.2.5/jubilee/vignettes/z-jubi-tut-unrate-yoy-1.tikz |only jubilee-0.3.1/jubilee/DESCRIPTION | 23 - jubilee-0.3.1/jubilee/MD5 | 105 ++-- jubilee-0.3.1/jubilee/NAMESPACE | 8 jubilee-0.3.1/jubilee/NEWS.md | 9 jubilee-0.3.1/jubilee/R/jubilee-constructor.R | 70 +++ jubilee-0.3.1/jubilee/R/jubilee-forward-rtn-method.R | 19 jubilee-0.3.1/jubilee/R/jubilee-macro-cost-method.R |only jubilee-0.3.1/jubilee/R/jubilee-macro-fit-method.R |only jubilee-0.3.1/jubilee/R/jubilee-macro-predict-method.R |only jubilee-0.3.1/jubilee/R/jubilee-optimal-tb3ms-method.R |only jubilee-0.3.1/jubilee/R/jubilee-package.R | 8 jubilee-0.3.1/jubilee/R/jubilee-read-fred-file.R | 23 - jubilee-0.3.1/jubilee/R/jubilee-repo-config.R | 105 ++++ jubilee-0.3.1/jubilee/R/jubilee-repo-constructor.R | 99 ++++ jubilee-0.3.1/jubilee/R/jubilee-yield-inversion-method.R |only jubilee-0.3.1/jubilee/inst/doc/jubilee-tutorial.ltx | 211 ++++++---- jubilee-0.3.1/jubilee/inst/doc/jubilee-tutorial.pdf |binary jubilee-0.3.1/jubilee/inst/extdata/B230RC0Q173SBEA.csv |only jubilee-0.3.1/jubilee/inst/extdata/BAA.csv | 10 jubilee-0.3.1/jubilee/inst/extdata/CAPUTLB00004SQ.csv |only jubilee-0.3.1/jubilee/inst/extdata/CES0500000035.csv |only jubilee-0.3.1/jubilee/inst/extdata/CES3000000035.csv |only jubilee-0.3.1/jubilee/inst/extdata/CP.csv |only jubilee-0.3.1/jubilee/inst/extdata/FEDFUNDS.csv |only jubilee-0.3.1/jubilee/inst/extdata/Fig3-1.xls |binary jubilee-0.3.1/jubilee/inst/extdata/GDP.csv |only jubilee-0.3.1/jubilee/inst/extdata/GDPC1.csv |only jubilee-0.3.1/jubilee/inst/extdata/GOLDAMGBD228NLBM.csv | 10 jubilee-0.3.1/jubilee/inst/extdata/IR3TED01USM156N.csv |only jubilee-0.3.1/jubilee/inst/extdata/POPTHM.csv |only jubilee-0.3.1/jubilee/inst/extdata/RECPROUSM156N.csv |only jubilee-0.3.1/jubilee/inst/extdata/TB3MS.csv | 10 jubilee-0.3.1/jubilee/inst/extdata/TCU.csv |only jubilee-0.3.1/jubilee/inst/extdata/UNRATE.csv | 10 jubilee-0.3.1/jubilee/inst/extdata/USREC.csv |only jubilee-0.3.1/jubilee/inst/extdata/ie_data.xls |binary jubilee-0.3.1/jubilee/man/jubilee-package.Rd | 9 jubilee-0.3.1/jubilee/man/jubilee.Rd | 5 jubilee-0.3.1/jubilee/man/jubilee.forward_rtn.Rd | 19 jubilee-0.3.1/jubilee/man/jubilee.macro_cost.Rd |only jubilee-0.3.1/jubilee/man/jubilee.macro_fit.Rd |only jubilee-0.3.1/jubilee/man/jubilee.macro_predict.Rd |only jubilee-0.3.1/jubilee/man/jubilee.optimal_tb3ms.Rd |only jubilee-0.3.1/jubilee/man/jubilee.read_fred_file.Rd | 5 jubilee-0.3.1/jubilee/man/jubilee.yield_inversion.Rd |only jubilee-0.3.1/jubilee/vignettes/jubilee-tutorial.ltx | 211 ++++++---- jubilee-0.3.1/jubilee/vignettes/pdf2ps.sh | 20 jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-20y-smr-GSI-plot-1.pdf |binary jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-20y-smr-YS-plot-1.pdf |binary jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-20y-smr-raw-plot-1.pdf |binary jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-demo-Yt-1.pdf |binary jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-forecast-10y-X-1.pdf |binary jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-forecast-10y-rtn-1.pdf |binary jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-forecast-20y-X-1.pdf |binary jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-forecast-20y-Y-1.pdf |only jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-forecast-20y-rtn-1.pdf |binary jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-inflation-1.pdf |binary jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-unrate-1.pdf |binary jubilee-0.3.1/jubilee/vignettes/z-jubi-tut-unrate-yoy-1.pdf |binary 72 files changed, 725 insertions(+), 264 deletions(-)
Title: A Small Message Queue for Parallel Processes
Description: This queue is a data structure that lets
parallel processes send and receive messages,
and it can help coordinate the work
of complicated parallel tasks.
Processes can push new messages to the queue,
pop old messages, and obtain a
log of all the messages ever pushed. File locking
preserves the integrity of the data even when
multiple processes access the queue simultaneously.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Ian E. Fellows [ctb],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between txtq versions 0.1.3 dated 2019-06-23 and 0.1.4 dated 2019-07-19
DESCRIPTION | 12 ++-- MD5 | 22 ++++---- NAMESPACE | 2 NEWS.md | 6 ++ R/assert.R |only R/package.R | 1 R/txtq.R | 108 ++++++++++++++++------------------------- R/utils.R |only README.md | 61 +++++++++++------------ inst/WORDLIST | 1 man/txtq.Rd | 7 +- tests/testthat/test-long.R |only tests/testthat/test-txtq.R | 66 +++---------------------- tests/testthat/test-validate.R |only 14 files changed, 111 insertions(+), 175 deletions(-)
Title: Sentiment Analysis Scorer
Description: Sentiment analysis is a popular technique in text mining that
attempts to determine the emotional state of some text. We provide a new
implementation of a common method for computing sentiment, whereby words are
scored as positive or negative according to a dictionary lookup. Then the
sum of those scores is returned for the document. We use the 'Hu' and 'Liu'
sentiment dictionary ('Hu' and 'Liu', 2004) <doi:10.1145/1014052.1014073>
for determining sentiment. The scoring function is 'vectorized' by document,
and scores for multiple documents are computed in parallel via 'OpenMP'.
Author: Drew Schmidt [aut, cre]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between meanr versions 0.1-1 dated 2017-10-26 and 0.1-2 dated 2019-07-19
meanr-0.1-1/meanr/src/Makevars |only meanr-0.1-2/meanr/ChangeLog | 8 meanr-0.1-2/meanr/DESCRIPTION | 23 meanr-0.1-2/meanr/LICENSE | 2 meanr-0.1-2/meanr/MD5 | 37 meanr-0.1-2/meanr/NAMESPACE | 3 meanr-0.1-2/meanr/R/meanr-package.r | 17 meanr-0.1-2/meanr/R/meanr.nthreads.r | 5 meanr-0.1-2/meanr/R/score.r | 25 meanr-0.1-2/meanr/README.md | 17 meanr-0.1-2/meanr/cleanup | 1 meanr-0.1-2/meanr/configure | 1309 ++++++++++++++++++++++++++++++- meanr-0.1-2/meanr/configure.ac | 28 meanr-0.1-2/meanr/inst/sexputils/RNACI.h | 224 +---- meanr-0.1-2/meanr/man/meanr-package.Rd | 16 meanr-0.1-2/meanr/man/meanr.nthreads.Rd | 3 meanr-0.1-2/meanr/man/score.Rd | 21 meanr-0.1-2/meanr/src/Makevars.in |only meanr-0.1-2/meanr/src/Makevars.win |only meanr-0.1-2/meanr/src/meanr_nthreads.c | 16 meanr-0.1-2/meanr/src/score.c | 4 21 files changed, 1517 insertions(+), 242 deletions(-)
Title: Statistical Disclosure Control for Spatial Data
Description: Privacy protected raster maps
can be created from spatial point data. Protection
methods include smoothing of dichotomous variables by de Jonge and de Wolf (2016)
<doi:10.1007/978-3-319-45381-1_9>, continuous variables by de Wolf and
de Jonge (2018) <doi:10.1007/978-3-319-99771-1_23>, suppressing
revealing values and a generalization of the quad tree method by
Suñé, Rovira, Ibáñez and Farré (2017) <doi:10.2901/EUROSTAT.C2017.001>.
Author: Edwin de Jonge [aut, cre] (<https://orcid.org/0000-0002-6580-4718>),
Peter-Paul de Wolf [aut],
Sapphire Han [ctb]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between sdcSpatial versions 0.1.0 dated 2019-07-03 and 0.1.1 dated 2019-07-19
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- R/protect_coarsen.R |only R/protect_quadtree.R | 14 +++++++++----- man/dwellings.Rd | 5 ++++- man/is_sensitive.Rd | 6 ++++-- man/protect_quadtree.Rd | 12 +++++++----- 7 files changed, 33 insertions(+), 21 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.4.2 dated 2019-06-11 and 0.4.3 dated 2019-07-19
DESCRIPTION | 8 MD5 | 60 - R/ARMA.R | 6 R/ARMA_optim.R | 2 R/Causation.R | 3 R/Dependence.R | 14 R/Dependence_base.R | 8 R/Dependence_matrix.R | 9 R/Internal_Functions.R | 2 R/Multivariate_Regression.R | 286 +++---- R/NNS_Distance.R | 5 R/Normalization.R | 4 R/Regression.R | 753 +++++++++----------- R/Stack.R | 22 R/dy_d_wrt.R | 3 R/dy_dx.R | 3 inst/doc/NNSvignette_Classification.R | 2 inst/doc/NNSvignette_Classification.Rmd | 2 inst/doc/NNSvignette_Classification.html | 16 inst/doc/NNSvignette_Clustering_and_Regression.R | 10 inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 14 inst/doc/NNSvignette_Clustering_and_Regression.html | 92 ++ man/NNS.ARMA.Rd | 6 man/NNS.ARMA.optim.Rd | 2 man/NNS.caus.Rd | 3 man/NNS.reg.Rd | 33 man/NNS.stack.Rd | 11 man/dy.d_.Rd | 3 man/dy.dx.Rd | 3 vignettes/NNSvignette_Classification.Rmd | 2 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 14 31 files changed, 743 insertions(+), 658 deletions(-)
Title: Check if the Title of a Package is Available, Appropriate and
Interesting
Description: Check if a given package name is available to use. It checks the
name's validity. Checks if it is used on 'GitHub', 'CRAN' and 'Bioconductor'. Checks
for unintended meanings by querying Urban Dictionary, 'Wiktionary' and Wikipedia.
Author: Carl Ganz [aut],
Gábor Csárdi [aut],
Jim Hester [aut, cre],
Molly Lewis [aut],
Rachael Tatman [aut]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between available versions 1.0.3 dated 2019-07-01 and 1.0.4 dated 2019-07-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ tests/testthat/test-badwords.R | 4 ++++ tests/testthat/test-bioc.R | 5 ++++- tests/testthat/test-cran.R | 4 ++++ tests/testthat/test-github.R | 4 ++++ 7 files changed, 29 insertions(+), 10 deletions(-)
Title: Automated Data Preparation
Description: Do most of the painful data preparation for a data science project with a minimum amount of code; Take advantages of data.table efficiency and use some algorithmic trick in order to perform data preparation in a time and RAM efficient way.
Author: Emmanuel-Lin Toulemonde [aut, cre]
Maintainer: Emmanuel-Lin Toulemonde <el.toulemonde@protonmail.com>
Diff between dataPreparation versions 0.4.0 dated 2019-03-25 and 0.4.1 dated 2019-07-19
DESCRIPTION | 6 MD5 | 167 - NAMESPACE | 106 NEWS | 375 +- NEWS.md | 375 +- R/aggregate.R | 376 +- R/datesManipulations.R | 942 +++--- R/discretization.R | 476 +-- R/generateFromCharacter.R | 162 - R/generateFromFactor.R | 633 ++-- R/genericFunctions.R | 832 ++--- R/prepareSet.R | 24 R/rowFiltering.R |only R/sameShape.R | 302 - R/setColAs.R | 780 ++-- R/shapeSet.R | 256 - R/whichFunctions.R | 728 ++-- build/vignette.rds |binary data/datalist | 4 inst/doc/dataPreparation.R | 320 +- inst/doc/dataPreparation.Rmd | 742 ++-- inst/doc/dataPreparation.html | 4375 ++++++++++++++-------------- inst/doc/train_test_prep.R | 160 - inst/doc/train_test_prep.Rmd | 494 +-- inst/doc/train_test_prep.html | 828 ++--- man/adult.Rd | 46 man/aggregateByKey.Rd | 116 man/as.POSIXct_fast.Rd | 56 man/build_bins.Rd | 80 man/build_encoding.Rd | 96 man/build_scales.Rd | 58 man/build_target_encoding.Rd |only man/dataPrepNews.Rd | 22 man/dateFormatUnifier.Rd | 70 man/description.Rd | 56 man/fastDiscretization.Rd | 94 man/fastFilterVariables.Rd | 86 man/fastHandleNa.Rd | 106 man/fastIsEqual.Rd | 70 man/fastRound.Rd | 84 man/fastScale.Rd | 106 man/findAndTransformDates.Rd | 150 man/findAndTransformNumerics.Rd | 92 man/generateDateDiffs.Rd | 102 man/generateFactorFromDate.Rd | 92 man/generateFromCharacter.Rd | 90 man/generateFromFactor.Rd | 88 man/identifyDates.Rd | 122 man/messy_adult.Rd | 48 man/one_hot_encoder.Rd | 102 man/prepareSet.Rd | 154 man/remove_percentile_outlier.Rd |only man/remove_rare_categorical.Rd |only man/remove_sd_outlier.Rd |only man/sameShape.Rd | 108 man/setAsNumericMatrix.Rd | 52 man/setColAsCharacter.Rd | 58 man/setColAsDate.Rd | 106 man/setColAsFactor.Rd | 78 man/setColAsNumeric.Rd | 84 man/shapeSet.Rd | 74 man/target_encode.Rd |only man/unFactor.Rd | 90 man/whichAreBijection.Rd | 88 man/whichAreConstant.Rd | 70 man/whichAreInDouble.Rd | 104 man/whichAreIncluded.Rd | 116 tests/testthat/test_aggregate.R | 308 - tests/testthat/test_datesManipulation.R | 662 ++-- tests/testthat/test_description.R | 64 tests/testthat/test_discretization.R | 514 +-- tests/testthat/test_factorManipulation.R | 106 tests/testthat/test_fastFunctions.R | 652 ++-- tests/testthat/test_fast_posixct.R | 36 tests/testthat/test_generateFromCharacter.R | 64 tests/testthat/test_generateFromDate.R | 444 +- tests/testthat/test_generateFromFactor.R | 270 + tests/testthat/test_genericFunctions.R | 1448 ++++----- tests/testthat/test_numericsManipulations.R | 246 - tests/testthat/test_prepareSet.R | 44 tests/testthat/test_rowFiltering.R |only tests/testthat/test_sameShape.R | 324 +- tests/testthat/test_scale.R | 326 +- tests/testthat/test_setColAs.R | 552 +-- tests/testthat/test_shapeSet.R | 234 - tests/testthat/test_whichFunctions.R | 422 +- vignettes/dataPreparation.Rmd | 742 ++-- vignettes/train_test_prep.Rmd | 494 +-- 88 files changed, 12459 insertions(+), 12170 deletions(-)
More information about dataPreparation at CRAN
Permanent link
Title: Robust Estimation and Inference in Sample Selection Models
Description: Package provides a set of tools for robust estimation and inference for models with sample selectivity.
Author: Mikhail Zhelonkin, Marc G. Genton, Elvezio Ronchetti
Maintainer: Mikhail Zhelonkin <Mikhail.Zhelonkin@gmail.com>
Diff between ssmrob versions 0.6 dated 2019-05-16 and 0.7 dated 2019-07-19
ssmrob-0.6/ssmrob/R/ssmrob-internal.R |only ssmrob-0.7/ssmrob/DESCRIPTION | 8 - ssmrob-0.7/ssmrob/MD5 | 57 ++++---- ssmrob-0.7/ssmrob/NAMESPACE | 21 ++- ssmrob-0.7/ssmrob/NEWS | 8 + ssmrob-0.7/ssmrob/R/etregrob.R | 6 ssmrob-0.7/ssmrob/R/heckit5rob.R | 7 + ssmrob-0.7/ssmrob/R/heckitrob.R | 15 +- ssmrob-0.7/ssmrob/R/model.matrix.etregrob.R |only ssmrob-0.7/ssmrob/R/model.matrix.heckit5rob.R |only ssmrob-0.7/ssmrob/R/model.matrix.heckitrob.R |only ssmrob-0.7/ssmrob/R/nobs.etregrob.R |only ssmrob-0.7/ssmrob/R/nobs.heckit5rob.R |only ssmrob-0.7/ssmrob/R/nobs.heckitrob.R |only ssmrob-0.7/ssmrob/R/print.etregrob.R | 12 + ssmrob-0.7/ssmrob/R/print.heckit5rob.R | 16 +- ssmrob-0.7/ssmrob/R/print.heckitrob.R | 12 + ssmrob-0.7/ssmrob/R/print.summary.etregrob.R | 14 +- ssmrob-0.7/ssmrob/R/print.summary.heckit5rob.R | 16 +- ssmrob-0.7/ssmrob/R/print.summary.heckitrob.R | 14 +- ssmrob-0.7/ssmrob/R/ssmrob.R | 9 + ssmrob-0.7/ssmrob/R/summary.etregrob.R | 9 + ssmrob-0.7/ssmrob/R/summary.heckit5rob.R | 15 +- ssmrob-0.7/ssmrob/R/summary.heckitrob.R | 10 + ssmrob-0.7/ssmrob/man/etregrob.Rd | 154 +++++++++++------------ ssmrob-0.7/ssmrob/man/heckit5rob.Rd | 13 + ssmrob-0.7/ssmrob/man/heckitrob.Rd | 8 - ssmrob-0.7/ssmrob/man/model.matrix.etregrob.Rd |only ssmrob-0.7/ssmrob/man/model.matrix.heckit5rob.Rd |only ssmrob-0.7/ssmrob/man/model.matrix.heckitrob.Rd |only ssmrob-0.7/ssmrob/man/nobs.heckitrob.Rd |only ssmrob-0.7/ssmrob/man/print.etregrob.Rd | 2 ssmrob-0.7/ssmrob/man/print.heckit5rob.Rd | 2 ssmrob-0.7/ssmrob/man/print.heckitrob.Rd | 2 ssmrob-0.7/ssmrob/man/ssmrob-package.Rd | 4 35 files changed, 274 insertions(+), 160 deletions(-)
Title: MNREAD Parameters Estimation and Curve Plotting
Description: Allows to analyze the reading data obtained with the MNREAD Acuity
Chart, a continuous-text reading acuity chart for normal and low vision.
Provides the necessary functions to plot the MNREAD curve and estimate
automatically the four MNREAD parameters: Maximum Reading Speed,
Critical Print Size, Reading Acuity and Reading Accessibility Index.
Parameters can be estimated either with the standard method
or with a nonlinear mixed-effects (NLME) modeling.
See Calabrese et al. 2018 for more details <doi.org/10.1167/18.1.8>.
Author: Aurélie Calabrèse [aut, cre],
J. Steve Mansfield [aut],
Gordon E. Legge [aut]
Maintainer: Aurélie Calabrèse <acalabre@umn.edu>
Diff between mnreadR versions 2.1.2 dated 2019-02-01 and 2.1.3 dated 2019-07-19
DESCRIPTION | 6 +++--- MD5 | 21 +++++++++++---------- NEWS.md |only R/acc_index.R | 3 ++- R/all_mnread_param.R | 12 ++++++------ R/curve_param.R | 8 ++++---- R/mnread_curve.R | 6 ++++-- R/nlme_curve.R | 42 +++++++++++++++++++++++++++++++++++++++++- R/zzz.R | 2 +- man/accIndex.Rd | 2 +- man/mnreadCurve.Rd | 6 ++++-- man/nlmeCurve.Rd | 42 +++++++++++++++++++++++++++++++++++++++++- 12 files changed, 118 insertions(+), 32 deletions(-)
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre],
Tom Drake [aut],
Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 0.9.2 dated 2019-05-31 and 0.9.4 dated 2019-07-19
DESCRIPTION | 6 +- MD5 | 83 ++++++++++++++++--------------- NAMESPACE | 5 + NEWS.md | 15 +++++ R/coefficient_plot.R | 21 ++++++- R/coxphmulti.R | 19 ++----- R/coxphuni.R | 13 ++++ R/ff_label.R | 1 R/finalfit.R | 14 +++-- R/finalfit_internal_functions.R | 54 +++++++++++++++++--- R/finalfit_package.R | 11 +++- R/glmmixed.R | 2 R/hr_plot.R | 31 +++++++++-- R/or_plot.R | 29 +++++++++- R/summaryfactorlist.R | 95 +++++++++++++++++++++++++----------- build/vignette.rds |binary inst/doc/all_tables_examples.html | 40 +++++++++++---- inst/doc/bootstrap.html | 26 ++++----- inst/doc/finalfit.html | 10 +++ inst/doc/missing.R | 2 inst/doc/missing.Rmd | 4 + inst/doc/missing.html | 46 +++++++++++++---- inst/doc/survival.R |only inst/doc/survival.Rmd |only inst/doc/survival.html |only man/coefficient_plot.Rd | 7 +- man/coxphmulti.Rd | 8 +-- man/coxphuni.Rd | 2 man/expositionpipe.Rd |only man/extract_fit.Rd | 24 +++++++++ man/format_n_percent.Rd | 4 + man/glmmixed.Rd | 2 man/hr_plot.Rd | 13 +++- man/or_plot.Rd | 7 +- man/summarise_categorical.Rd | 2 man/summarise_continuous.Rd | 2 man/summary_factorlist.Rd | 13 +++- man/summary_factorlist0.Rd | 9 +-- man/summary_factorlist_groups.Rd | 10 +-- tests/testthat/Rplots.pdf |binary tests/testthat/test_all_in_one.R | 12 ++++ tests/testthat/test_modelwrappers.R | 2 tests/testthat/test_plots.R | 10 +++ vignettes/missing.Rmd | 4 + vignettes/survival.Rmd |only 45 files changed, 472 insertions(+), 186 deletions(-)
Title: For Implementation of Feed Reduction, Learning Examples, NLP and
Code Management
Description: This is for code management functions, NLP tools, a Monty Hall simulator, and for implementing my own variable reduction technique called Feed Reduction <http://wbbpredictions.com/wp-content/uploads/2018/12/Redditbot_Paper.pdf>. The Feed Reduction technique is not yet published, but is merely a tool for implementing a series of binary neural networks meant for reducing data into N dimensions, where N is the number of possible values of the response variable.
Author: Travis Barton (2018)
Maintainer: Travis Barton <travis.barton@sjsu.edu>
Diff between LilRhino versions 0.1.0 dated 2019-03-13 and 1.1.0 dated 2019-07-19
DESCRIPTION | 15 +++++----- MD5 | 14 ++++++--- NAMESPACE | 11 ++++++- R/Personal_Functions.R | 71 ++++++++++++++++++++++++++++++++++++++++++++++++- README.md |only man/Binary_Network.Rd | 25 +++++++++-------- man/Feed_Reduction.Rd | 37 ++++++++++++++----------- man/Num_Al_Sep.Rd |only man/Pretreatment.Rd |only man/Stopword_Maker.Rd |only 10 files changed, 132 insertions(+), 41 deletions(-)
Title: Conventional and Fuzzy Data Envelopment Analysis
Description: Set of functions for Data Envelopment Analysis. It runs both classic and fuzzy DEA models.See: Banker, R.; Charnes, A.; Cooper, W.W. (1984). <doi:10.1287/mnsc.30.9.1078>, Charnes, A.; Cooper, W.W.; Rhodes, E. (1978). <doi:10.1016/0377-2217(78)90138-8> and Charnes, A.; Cooper, W.W.; Rhodes, E. (1981). <doi:10.1287/mnsc.27.6.668>.
Author: Vicente Coll-Serrano, Vicente Bolos, Rafael Benitez Suarez <rabesua@uv.es>
Maintainer: Vicente Bolos <vicente.bolos@uv.es>
Diff between deaR versions 1.0 dated 2018-12-23 and 1.1.0 dated 2019-07-19
DESCRIPTION | 12 MD5 | 156 ++--- NAMESPACE | 5 R/bootstrap_basic.R | 22 R/cross_efficiency.R | 19 R/cross_efficiency_fuzzy.R | 9 R/data_sets.R | 141 ++++ R/efficiencies.R | 4 R/efficiencies.dea.R | 13 R/efficiencies.dea_fuzzy.R | 16 R/lambdas.R | 9 R/malmquist_index.R | 673 +++++++++++++++++++--- R/model_additive.R | 674 +++++++++++----------- R/model_addsupereff.R | 718 ++++++++++++------------ R/model_basic.R | 99 ++- R/model_deaps.R | 771 ++++++++++++------------- R/model_fdh.R | 23 R/model_multiplier.R | 38 - R/model_nonradial.R | 32 - R/model_profit.R |only R/model_rdm.R |only R/model_sbmcomposite.R |only R/model_sbmeff.R | 66 +- R/model_sbmsupereff.R | 166 ++--- R/model_supereff.R | 8 R/modelfuzzy_guotanaka.R | 552 +++++++++--------- R/modelfuzzy_kaoliu.R | 25 R/modelfuzzy_possibilistic.R | 443 +++++++------- R/multipliers.R | 1 R/plot.dea.R | 631 ++++++++++++--------- R/plot.deafuzzy.R |only R/read_data.R | 208 ++++-- R/read_data_fuzzy.R | 358 ++++++++--- R/read_malmquist.R | 27 R/references.R | 4 R/rts.R | 218 +++---- R/slacks.R | 5 R/summary.dea.R | 688 +++++++++++++++-------- R/summary.deafuzzy.R | 1195 ++++++++++++++++++++++++---------------- R/targets.R | 1 R/undesirable_basic.R | 4 data/Coelli_1998.RData |only data/Fortune500.RData |binary data/Grifell_Lovell_1999.RData |only data/Tone2003.RData |only man/Coelli_1998.Rd |only man/Fortune500.Rd | 2 man/Grifell_Lovell_1999.Rd |only man/Tone2001.Rd | 2 man/Tone2003.Rd |only man/bootstrap_basic.Rd | 22 man/cross_efficiency.Rd | 19 man/cross_efficiency_fuzzy.Rd | 9 man/efficiencies.dea.Rd | 10 man/efficiencies.dea_fuzzy.Rd | 10 man/lambdas.Rd | 9 man/malmquist_index.Rd | 82 ++ man/model_additive.Rd | 28 man/model_addsupereff.Rd | 28 man/model_basic.Rd | 16 man/model_deaps.Rd | 2 man/model_fdh.Rd | 6 man/model_multiplier.Rd | 22 man/model_nonradial.Rd | 25 man/model_profit.Rd |only man/model_rdm.Rd |only man/model_sbmcomposite.Rd |only man/model_sbmeff.Rd | 36 - man/model_sbmsupereff.Rd | 36 - man/model_supereff.Rd | 8 man/modelfuzzy_guotanaka.Rd | 10 man/modelfuzzy_kaoliu.Rd | 17 man/modelfuzzy_possibilistic.Rd | 9 man/multipliers.Rd | 1 man/plot.dea.Rd | 7 man/plot.dea_fuzzy.Rd |only man/read_data.Rd | 43 + man/read_data_fuzzy.Rd | 81 +- man/read_malmquist.Rd | 7 man/references.Rd | 4 man/rts.Rd | 12 man/slacks.Rd | 1 man/summary.dea.Rd | 14 man/summary.dea_fuzzy.Rd | 8 man/targets.Rd | 1 man/undesirable_basic.Rd | 4 86 files changed, 5166 insertions(+), 3459 deletions(-)
Title: Moments of Folded and Doubly Truncated Multivariate
Distributions
Description: It computes the raw moments for the truncated and folded multivariate normal, Skew-normal (SN), Extended skew normal (ESN) and Student's t-distribution. It also offers specific functions to compute the mean and variance-covariance matrix as well as the cumulative distribution function (cdf) for the folded normal, SN, ESN, and folded t-distribution. Density and random deviates are offered for the ESN (SN as particular case) distribution. Most algorithms are extensions based on Kan, R., & Robotti, C. (2017) <doi:10.1080/10618600.2017.1322092>.
Author: Christian E. Galarza, Victor H. Lachos
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between MomTrunc versions 2.37 dated 2019-05-07 and 3.19 dated 2019-07-19
DESCRIPTION | 10 ++-- MD5 | 69 ++++++++++++++++++---------------- NAMESPACE | 6 +- R/AUX_correctors.R |only R/AUX_esn.R | 70 ++++++++++++++++++++++++---------- R/AUX_qfuns.R | 31 ++++++++++++++- R/AUX_t.R |only R/ESN_mv.R | 105 ++++++++++++++++++++++++++++++++-------------------- R/FESN1_mv.R | 6 ++ R/FESN_mom.R | 14 ++++-- R/FESN_mv.R | 10 +++- R/FN_mv.R | 2 R/TESN1_mean.R | 9 +++- R/TESN1_mv.R | 9 +++- R/TESN_mom.R | 21 ++++++---- R/TESN_mv.R | 48 ++++++++++++++++++----- R/TN1_mean.R | 14 ++++-- R/TN1_mv.R | 20 ++++++--- R/TN_mom.R | 6 +- R/TN_mv.R | 39 ++++++++++++++----- R/TN_mv_Kan.R | 56 ++++++++++++++++++++++----- R/TN_mv_Vaida.R | 84 +++++++++++++++++++++++++++++------------ R/TT_mean.R | 16 ------- R/TT_mv.R | 6 +- R/USER_cdfFMD.R | 2 R/USER_dmvESN.R |only R/USER_meanvarFMD.R | 2 R/USER_meanvarTMD.R | 16 ------- R/USER_momentsFMD.R | 2 R/USER_momentsTMD.R | 2 R/USER_pmvESN.R |only R/USER_rmvESN.R |only man/cdfFMD.Rd | 2 man/drmvESN.Rd |only man/meanvarFMD.Rd | 5 +- man/meanvarTMD.Rd | 4 - man/momentsFMD.Rd | 5 +- man/momentsTMD.Rd | 5 +- man/pmvESN.Rd |only 39 files changed, 460 insertions(+), 236 deletions(-)
Title: Infers Novel Immunoglobulin Alleles from Sequencing Data
Description: Infers the V genotype of an individual from immunoglobulin (Ig)
repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of
any novel alleles. This information is then used to correct existing V
allele calls from among the sample sequences.
Citations:
Gadala-Maria, et al (2015) <doi:10.1073/pnas.1417683112>.
Author: Daniel Gadala-Maria [aut],
Susanna Marquez [aut],
Moriah Cohen [aut],
Gur Yaari [aut],
Jason Vander Heiden [ctb, cre],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between tigger versions 0.3.1 dated 2018-10-19 and 0.4.0 dated 2019-07-19
DESCRIPTION | 16 MD5 | 59 +-- NAMESPACE | 23 - NEWS.md | 24 + R/bayesian.R | 103 ++--- R/data.R | 53 ++ R/evidence.R | 24 - R/functions.R | 784 +++++++++++++++++++++++++---------------- R/tigger.R | 23 - build/vignette.rds |binary data/SampleGermlineIGHV.rda |only data/airrDb.rda |only data/datalist | 2 inst/CITATION | 2 inst/doc/Tigger-Vignette.R | 7 inst/doc/Tigger-Vignette.Rmd | 19 inst/doc/Tigger-Vignette.pdf |binary man/GermlineIGHV.Rd | 5 man/SampleDb.Rd | 3 man/SampleGermlineIGHV.Rd |only man/airrDb.Rd |only man/findNovelAlleles.Rd | 32 + man/findUnmutatedCalls.Rd | 2 man/generateEvidence.Rd | 19 man/genotypeFasta.Rd | 2 man/getMutCount.Rd | 12 man/getPopularMutationCount.Rd | 14 man/inferGenotype.Rd | 13 man/inferGenotypeBayesian.Rd | 12 man/plotNovel.Rd | 18 man/reassignAlleles.Rd | 10 man/subsampleDb.Rd |only vignettes/Tigger-Vignette.Rmd | 19 33 files changed, 846 insertions(+), 454 deletions(-)
Title: Fitting Semi-Parametric Generalized log-Gamma Regression Models
Description: Set of tools to fit a linear multiple or semi-parametric regression
models and non-informative right-censoring may be considered. Under this setup, the localization parameter of the response variable distribution is modeled by using linear multiple regression
or semi-parametric functions, whose non-parametric components may be approximated
by natural cubic spline or P-splines. The supported distribution for the model error is a generalized log-gamma distribution which includes
the generalized extreme value distribution as an important special case.
Author: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com> and G. Paula and L. Vanegas
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between sglg versions 0.1.4 dated 2019-02-20 and 0.1.5 dated 2019-07-19
sglg-0.1.4/sglg/R/plot.sglg.R |only sglg-0.1.4/sglg/man/plot.sglg.Rd |only sglg-0.1.5/sglg/DESCRIPTION | 10 sglg-0.1.5/sglg/MD5 | 52 ++-- sglg-0.1.5/sglg/NAMESPACE | 6 sglg-0.1.5/sglg/R/blockgs.R | 61 +++- sglg-0.1.5/sglg/R/deviance_residuals.R |only sglg-0.1.5/sglg/R/envelope.sglg.R | 48 +-- sglg-0.1.5/sglg/R/glg.R | 168 ++++++------- sglg-0.1.5/sglg/R/gnfit.R | 28 +- sglg-0.1.5/sglg/R/influence.sglg.R | 183 ++++++++------ sglg-0.1.5/sglg/R/kmpar.R | 25 +- sglg-0.1.5/sglg/R/order_glg.R | 29 ++ sglg-0.1.5/sglg/R/plot.npc.R | 144 +++++------ sglg-0.1.5/sglg/R/quantile_residuals.R |only sglg-0.1.5/sglg/R/sglg2.R | 358 ++++++++++++++--------------- sglg-0.1.5/sglg/R/shape.R | 31 +- sglg-0.1.5/sglg/R/survglg.R | 1 sglg-0.1.5/sglg/man/deviance_residuals.Rd |only sglg-0.1.5/sglg/man/envelope.sglg.Rd | 8 sglg-0.1.5/sglg/man/glg.Rd | 2 sglg-0.1.5/sglg/man/gnfit.Rd | 9 sglg-0.1.5/sglg/man/influence.sglg.Rd | 3 sglg-0.1.5/sglg/man/order_glg.Rd | 28 ++ sglg-0.1.5/sglg/man/plotnpc.Rd | 56 +--- sglg-0.1.5/sglg/man/quantile_residuals.Rd |only sglg-0.1.5/sglg/man/sglg.Rd | 52 +--- sglg-0.1.5/sglg/man/survglg.Rd | 1 sglg-0.1.5/sglg/tests/testthat/test_glg.R | 4 sglg-0.1.5/sglg/tests/testthat/test_sglg.R | 4 30 files changed, 715 insertions(+), 596 deletions(-)
Title: Connectivity to 'Alfresco' Content Management Repositories
Description: Allows you to connect to an 'Alfresco' content management repository and interact
with its contents using simple and intuitive functions. You will be able to establish a connection session to the 'Alfresco' repository,
read and upload content and manage folder hierarchies. For more details on the 'Alfresco' content management repository
see <https://www.alfresco.com/ecm-software/document-management>.
Author: Roy Wetherall <rwetherall@gmail.com>
Maintainer: Roy Wetherall <rwetherall@gmail.com>
Diff between alfr versions 1.2.0 dated 2019-07-09 and 1.2.1 dated 2019-07-19
alfr-1.2.0/alfr/R/sysdata.rda |only alfr-1.2.0/alfr/tests/testthat/resources |only alfr-1.2.1/alfr/DESCRIPTION | 6 +++--- alfr-1.2.1/alfr/MD5 | 9 +++------ alfr-1.2.1/alfr/NEWS.md | 4 ++++ alfr-1.2.1/alfr/tests/testthat/testalf_session.R | 10 ++++++++-- 6 files changed, 18 insertions(+), 11 deletions(-)