Title: Advanced 'tryCatch()' and 'try()' Functions
Description: Advanced tryCatch() and try() functions for better error handling
(logging, stack trace with source code references and support for post-mortem analysis via dump files).
Author: Juergen Altfeld [aut, cre, cph],
Charles Epaillard [ctb]
Maintainer: Juergen Altfeld <jaltfeld@altfeld-im.de>
Diff between tryCatchLog versions 1.1.2 dated 2019-03-20 and 1.1.4 dated 2019-03-25
DESCRIPTION | 12 +-- MD5 | 21 +++--- NEWS.md | 20 +++++- R/is_package_available.R | 4 - R/zzz.R | 46 +++++++++++--- inst/doc/tryCatchLog-intro.html | 4 - man/is.package.available.Rd | 4 - tests/testthat/test_dump_files.R | 2 tests/testthat/test_is_duplicated_log_entry.R | 8 +- tests/testthat/test_last_tryCatchLog_result.R | 2 tests/testthat/test_namespace_hooks.R | 7 +- tests/testthat/test_zzz_call_without_attaching_issue_41.R |only 12 files changed, 94 insertions(+), 36 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from
National Water Information System (NWIS) <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>.
Both EPA and USGS water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Laura DeCicco [aut, cre] (<https://orcid.org/0000-0002-3915-9487>),
Robert Hirsch [aut] (<https://orcid.org/0000-0002-4534-075X>),
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Carr [ctb],
David Watkins [aut] (<https://orcid.org/0000-0002-7544-0700>)
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.3 dated 2017-09-28 and 2.7.4 dated 2019-03-25
DESCRIPTION | 27 MD5 | 60 - NAMESPACE | 24 R/checkWQPdates.r | 3 R/getWebServiceData.R | 38 R/importNGWMN_wml2.R | 27 R/importRDB1.r | 47 R/importWQP.R | 26 R/importWaterML1.r | 28 R/readNGWMNdata.R | 13 R/readNWISdata.r | 17 R/readNWISdv.r | 1 R/readNWISqw.r | 11 R/readNWISunit.r | 24 R/renameColumns.R | 5 R/whatNWISData.r | 5 R/whatNWISsites.R | 3 R/whatWQPdata.R | 12 build/vignette.rds |binary inst/CITATION | 19 inst/doc/dataRetrieval.html | 1798 +++++++++++++++++++++---------- man/constructWQPURL.Rd | 3 man/importRDB1.Rd | 3 man/importWaterML1.Rd | 2 man/readNWISgwl.Rd | 4 man/readNWISpeak.Rd | 4 man/renameNWISColumns.Rd | 5 man/stateCdLookup.Rd | 2 tests/testthat/tests_general.R | 19 tests/testthat/tests_imports.R | 55 tests/testthat/tests_userFriendly_fxns.R | 2 31 files changed, 1460 insertions(+), 827 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for multiple random effects and estimation of unknown variance-covariance structures (i.e. heterogeneous and unstructured variance models) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) to include multiple known relationship matrices and estimate complex unknown covariance structures. Spatial models can be fitted using the two-dimensional spline functionality in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 3.8 dated 2019-01-02 and 3.9.1 dated 2019-03-25
CHANGELOG | 19 DESCRIPTION | 8 MD5 | 74 +-- R/FUN_emmeans.R |only R/FUN_markers.R | 126 +++-- R/FUN_relationships.R | 23 R/FUN_special.R | 98 ++-- R/FUN_utils.R | 68 +- R/mmer.R | 46 + build/vignette.rds |binary inst/doc/sommer.FAQ.R |only inst/doc/sommer.FAQ.Rmd |only inst/doc/sommer.FAQ.pdf |only inst/doc/sommer.R | 4 inst/doc/sommer.Rmd | 4 inst/doc/sommer.changes.Rmd |only inst/doc/sommer.changes.pdf |only inst/doc/sommer.pdf |binary inst/doc/sommer.start.R | 152 ++---- inst/doc/sommer.start.Rmd | 443 ++++++++++-------- inst/doc/sommer.start.pdf |binary man/GWAS.Rd | 51 +- man/atcg1234.Rd | 3 man/fcm.Rd | 7 man/fixm.Rd | 6 man/leg.Rd | 2 man/mmer.Rd | 37 - man/overlay.Rd | 2 man/pedtoK.Rd | 7 man/predict.Rd | 3 man/sommer-package.Rd | 2 man/uncm.Rd | 5 man/unsm.Rd | 6 man/vs.Rd | 40 + src/MNR.cpp | 6 vignettes/sommer.FAQ.Rmd |only vignettes/sommer.FAQ.html |only vignettes/sommer.Rmd | 4 vignettes/sommer.changes.Rmd |only vignettes/sommer.changes.html |only vignettes/sommer.html | 468 +++++++++----------- vignettes/sommer.start.Rmd | 443 ++++++++++-------- vignettes/sommer.start.html | 981 +++++++++++++++++------------------------- 43 files changed, 1585 insertions(+), 1553 deletions(-)
Title: Connect to 'R-hub'
Description: Run 'R CMD check' on any of the 'R-hub' (<https://builder.r-hub.io/>)
architectures, from the command line. The current architectures include
'Windows', 'macOS', 'Solaris' and various 'Linux' distributions.
Author: Gábor Csárdi [aut, cre],
Maëlle Salmon [aut] (<https://orcid.org/0000-0002-2815-0399>),
R Consortium [fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between rhub versions 1.0.2 dated 2017-11-02 and 1.1.0 dated 2019-03-25
rhub-1.0.2/rhub/R/check-list-class.R |only rhub-1.0.2/rhub/inst/README.markdown |only rhub-1.0.2/rhub/inst/check-output.gif |only rhub-1.0.2/rhub/inst/email-validation.png |only rhub-1.1.0/rhub/DESCRIPTION | 38 +-- rhub-1.1.0/rhub/LICENSE | 4 rhub-1.1.0/rhub/MD5 | 86 ++++-- rhub-1.1.0/rhub/NAMESPACE | 39 ++- rhub-1.1.0/rhub/NEWS.md | 32 ++ rhub-1.1.0/rhub/R/api.R | 35 +- rhub-1.1.0/rhub/R/assertions.R | 15 + rhub-1.1.0/rhub/R/check-class.R | 304 ++++++++++++++++++++++-- rhub-1.1.0/rhub/R/check-cran.R | 2 rhub-1.1.0/rhub/R/check-shortcuts.R | 14 - rhub-1.1.0/rhub/R/check.R | 22 - rhub-1.1.0/rhub/R/column-dt.R |only rhub-1.1.0/rhub/R/column-group-id.R |only rhub-1.1.0/rhub/R/column-id.R |only rhub-1.1.0/rhub/R/column-result.R |only rhub-1.1.0/rhub/R/column-status.R |only rhub-1.1.0/rhub/R/email.R | 14 - rhub-1.1.0/rhub/R/env.R | 51 +++- rhub-1.1.0/rhub/R/handle.R | 6 rhub-1.1.0/rhub/R/list.R | 102 ++++++-- rhub-1.1.0/rhub/R/local.R |only rhub-1.1.0/rhub/R/platform.R | 6 rhub-1.1.0/rhub/R/print-status.R | 9 rhub-1.1.0/rhub/R/print.R | 32 ++ rhub-1.1.0/rhub/R/rhub-package.R |only rhub-1.1.0/rhub/R/utils.R | 41 +++ rhub-1.1.0/rhub/build/rhub.pdf |binary rhub-1.1.0/rhub/build/vignette.rds |only rhub-1.1.0/rhub/inst/bin |only rhub-1.1.0/rhub/inst/doc |only rhub-1.1.0/rhub/man/check.Rd | 12 rhub-1.1.0/rhub/man/check_for_cran.Rd | 4 rhub-1.1.0/rhub/man/check_shortcuts.Rd | 8 rhub-1.1.0/rhub/man/figures |only rhub-1.1.0/rhub/man/get_check.Rd |only rhub-1.1.0/rhub/man/list_my_checks.Rd | 36 ++ rhub-1.1.0/rhub/man/list_package_checks.Rd | 32 ++ rhub-1.1.0/rhub/man/list_validated_emails.Rd | 5 rhub-1.1.0/rhub/man/local_check_linux.Rd |only rhub-1.1.0/rhub/man/local_check_linux_images.Rd |only rhub-1.1.0/rhub/man/platforms.Rd | 2 rhub-1.1.0/rhub/man/rhub-ids.Rd |only rhub-1.1.0/rhub/man/rhub-package.Rd |only rhub-1.1.0/rhub/man/rhub_check.Rd | 69 +---- rhub-1.1.0/rhub/man/validate_email.Rd | 7 rhub-1.1.0/rhub/vignettes |only 50 files changed, 816 insertions(+), 211 deletions(-)
Title: Performs Quality Control, Data Normalization, and Batch Effect
Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and
batch effect correction operations for 'NanoString nCounter' data,
Talhouk et al. (2016) <doi:10.1371/journal.pone.0153844>. Various
metrics are used to determine which samples passed or failed QC. Gene
expression should first be normalized to housekeeping genes, before a
reference-based approach is used to adjust for batch effects. Raw
NanoString data can be imported in the form of Reporter Code Count
(RCC) files.
Author: Derek Chiu [aut, cre],
Aline Talhouk [aut],
Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between nanostringr versions 0.1.0 dated 2019-03-15 and 0.1.1 dated 2019-03-25
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS.md | 6 +++++- inst/CITATION |only inst/doc/Overview.html | 8 ++++---- 5 files changed, 17 insertions(+), 12 deletions(-)
Title: Reading Annual Financial Reports from Bovespa's DFP, FRE and FCA
System
Description: Reads annual financial reports including assets, liabilities, dividends history, stockholder composition and much more from Bovespa's DFP, FRE and FCA systems <http://www.bmfbovespa.com.br/en_us/products/listed-equities-and-derivatives/equities/listed-companies.htm>.
These are web based interfaces for all financial reports of companies traded at Bovespa. The package is specially designed for large scale data importation, keeping a tabular (long) structure for easier processing.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetDFPData versions 1.5 dated 2019-02-14 and 1.5.1 dated 2019-03-25
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/gdfpd_GetDFPData.R | 3 +-- build/vignette.rds |binary inst/doc/gdfpd-vignette-introduction.html | 9 ++++++--- 6 files changed, 20 insertions(+), 14 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, following Marcon, Traissac, Puech, and Lang (2015) <doi:10.18637/jss.v067.c03>.
Includes classical functions (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M).
Relies on 'spatstat' for some core calculation.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>),
Gabriel Lang [aut] (<https://orcid.org/0000-0002-4325-6044>),
Stephane Traissac [aut],
Florence Puech [aut] (<https://orcid.org/0000-0002-5279-6878>)
Maintainer: Eric Marcon <eric.marcon@ecofog.gf>
Diff between dbmss versions 2.6-3 dated 2018-03-19 and 2.7-0 dated 2019-03-25
dbmss-2.6-3/dbmss/inst/doc/docs.Rmd |only dbmss-2.6-3/dbmss/inst/doc/docs.html |only dbmss-2.6-3/dbmss/inst/doc/rd.Rmd |only dbmss-2.6-3/dbmss/inst/doc/rd.html |only dbmss-2.6-3/dbmss/vignettes/CSBIGS.Rdata |only dbmss-2.6-3/dbmss/vignettes/dbmss.bib |only dbmss-2.6-3/dbmss/vignettes/docs.Rmd |only dbmss-2.6-3/dbmss/vignettes/rd.Rmd |only dbmss-2.6-3/dbmss/vignettes/rd_index.yaml |only dbmss-2.7-0/dbmss/DESCRIPTION | 32 +++++++------- dbmss-2.7-0/dbmss/MD5 | 42 ++++++++---------- dbmss-2.7-0/dbmss/NAMESPACE | 9 ++- dbmss-2.7-0/dbmss/NEWS.md | 68 ++++++++++++++++++------------ dbmss-2.7-0/dbmss/R/Kdhat.R | 44 ++++++++----------- dbmss-2.7-0/dbmss/R/KinhomEnvelope.R | 2 dbmss-2.7-0/dbmss/R/Kmmhat.R | 4 - dbmss-2.7-0/dbmss/R/autoplot.R |only dbmss-2.7-0/dbmss/R/ghat.R | 2 dbmss-2.7-0/dbmss/R/m_hat.R | 11 ++-- dbmss-2.7-0/dbmss/README.md | 10 +--- dbmss-2.7-0/dbmss/build/vignette.rds |binary dbmss-2.7-0/dbmss/inst/doc/dbmss.R |only dbmss-2.7-0/dbmss/inst/doc/dbmss.Rmd |only dbmss-2.7-0/dbmss/inst/doc/dbmss.html |only dbmss-2.7-0/dbmss/man/Kdhat.Rd | 5 ++ dbmss-2.7-0/dbmss/man/autoplot.Rd |only dbmss-2.7-0/dbmss/man/figures |only dbmss-2.7-0/dbmss/man/m_hat.Rd | 5 ++ dbmss-2.7-0/dbmss/tests/testthat/testKd.R | 7 --- dbmss-2.7-0/dbmss/vignettes/dbmss.Rmd |only 30 files changed, 129 insertions(+), 112 deletions(-)
Title: Descriptive mAchine Learning EXplanations
Description: Machine Learning (ML) models are widely used and have various applications in classification
or regression. Models created with boosting, bagging, stacking or similar techniques are often
used due to their high performance, but such black-box models usually lack of interpretability.
DALEX package contains various explainers that help to understand the link between input variables and model output.
The single_variable() explainer extracts conditional response of a model as a function of a single selected variable.
It is a wrapper over packages 'pdp' (Greenwell 2017) <doi:10.32614/RJ-2017-016>,
'ALEPlot' (Apley 2018) <arXiv:1612.08468> and 'factorMerger' (Sitko and Biecek 2017) <arXiv:1709.04412>.
The single_prediction() explainer attributes parts of a model prediction to particular variables used in the model.
It is a wrapper over 'breakDown' package (Staniak and Biecek 2018) <doi:10.32614/RJ-2018-072>.
The variable_dropout() explainer calculates variable importance scores based on variable shuffling
(Fisher at al. 2018) <arXiv:1801.01489>.
All these explainers can be plotted with generic plot() function and compared across different models.
'DALEX' is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between DALEX versions 0.2.7 dated 2019-03-03 and 0.3.0 dated 2019-03-25
DESCRIPTION | 20 ++++-- MD5 | 76 +++++++++++++++----------- NAMESPACE | 22 ++++--- NEWS.md | 19 ++++++ R/apartments.R | 2 R/explain.R | 78 --------------------------- R/install_dependencies.R |only R/loss_functions.R |only R/model_performance.R | 19 +++--- R/plot_model_feature_response.R |only R/plot_model_performance.R | 28 ++++----- R/plot_single_prediction.R | 34 +++++++---- R/plot_single_variable.R | 72 ++++++++++++------------ R/plot_variable_dropout.R | 48 +++++++++------- R/predict_explainer.R |only R/single_feature.R |only R/single_prediction.R | 8 +- R/single_variable.R | 43 ++++++++------ R/theme_drwhy.R |only R/titanic.R |only R/variable_dropout.R | 42 ++------------ R/yhat.R |only R/zzz.R | 3 - data/titanic.rda |only man/apartments.Rd | 2 man/install_dependencies.Rd |only man/loss_cross_entropy.Rd | 7 +- man/model_feature_response.Rd |only man/model_performance.Rd | 16 +++-- man/plot.model_feature_response_explainer.Rd |only man/plot.model_performance_explainer.Rd | 13 ++-- man/plot.prediction_breakdown_explainer.Rd | 6 +- man/plot.variable_importance_explainer.Rd | 31 ++++++---- man/plot.variable_response_explainer.Rd | 29 ++++------ man/predict.Rd |only man/prediction_breakdown.Rd | 9 ++- man/print.model_performance_explainer.Rd | 4 - man/theme_drwhy.Rd |only man/titanic.Rd |only man/variable_importance.Rd | 17 +++-- man/variable_response.Rd | 36 +++++++----- man/yhat.Rd | 2 tests/testthat/helper-objects.R | 17 ++--- tests/testthat/test_explain.R | 2 tests/testthat/test_prediction_breakdown.R | 2 tests/testthat/test_single_feature.R |only tests/testthat/test_variable_response.R | 12 ++-- 47 files changed, 352 insertions(+), 367 deletions(-)
Title: An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Description: An Arsenal of 'R' functions for large-scale statistical summaries,
which are streamlined to work within the latest reporting tools in 'R' and
'RStudio' and which use formulas and versatile summary statistics for summary
tables and models. The primary functions include tableby(), a Table-1-like
summary of multiple variable types 'by' the levels of one or more categorical
variables; paired(), a Table-1-like summary of multiple variable types paired across
two time points; modelsum(), which performs simple model fits on one or more endpoints
for many variables (univariate or adjusted for covariates);
freqlist(), a powerful frequency table across many categorical variables;
comparedf(), a function for comparing data.frames; and
write2(), a function to output tables to a document.
Author: Ethan Heinzen [aut, cre],
Jason Sinnwell [aut],
Elizabeth Atkinson [aut],
Tina Gunderson [aut],
Gregory Dougherty [aut],
Patrick Votruba [ctb],
Ryan Lennon [ctb],
Andrew Hanson [ctb],
Krista Goergen [ctb],
Emily Lundt [ctb],
Brendan Broderick [ctb],
Maddie McCullough [art]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between arsenal versions 2.0.0 dated 2019-01-16 and 3.0.0 dated 2019-03-25
arsenal-2.0.0/arsenal/R/compare.data.frame.R |only arsenal-2.0.0/arsenal/R/compare.internal.R |only arsenal-2.0.0/arsenal/R/comparison.control.R |only arsenal-2.0.0/arsenal/R/comparison.tolerances.R |only arsenal-2.0.0/arsenal/R/summary.compare.R |only arsenal-2.0.0/arsenal/inst/doc/compare.R |only arsenal-2.0.0/arsenal/inst/doc/compare.Rmd |only arsenal-2.0.0/arsenal/inst/doc/compare.html |only arsenal-2.0.0/arsenal/man/compare.data.frame.Rd |only arsenal-2.0.0/arsenal/man/comparison.control.Rd |only arsenal-2.0.0/arsenal/man/comparison.tolerances.Rd |only arsenal-2.0.0/arsenal/tests/testthat/test_compare.R |only arsenal-2.0.0/arsenal/vignettes/compare.Rmd |only arsenal-3.0.0/arsenal/DESCRIPTION | 10 arsenal-3.0.0/arsenal/MD5 | 161 +++++++------- arsenal-3.0.0/arsenal/NAMESPACE | 36 ++- arsenal-3.0.0/arsenal/NEWS.md | 57 +++++ arsenal-3.0.0/arsenal/R/arsenal.R | 4 arsenal-3.0.0/arsenal/R/arsenal_table.R | 18 + arsenal-3.0.0/arsenal/R/as.data.frame.tableby.R | 12 - arsenal-3.0.0/arsenal/R/comparedf.R |only arsenal-3.0.0/arsenal/R/comparedf.control.R |only arsenal-3.0.0/arsenal/R/comparedf.internal.R |only arsenal-3.0.0/arsenal/R/comparedf.tolerances.R |only arsenal-3.0.0/arsenal/R/defunct.R |only arsenal-3.0.0/arsenal/R/deprecated.R |only arsenal-3.0.0/arsenal/R/formulize.R | 19 + arsenal-3.0.0/arsenal/R/freq.control.R | 2 arsenal-3.0.0/arsenal/R/freqlist.R | 18 + arsenal-3.0.0/arsenal/R/freqlist.internal.R | 65 ++++- arsenal-3.0.0/arsenal/R/internal.functions.R | 1 arsenal-3.0.0/arsenal/R/keep.labels.R | 41 +++ arsenal-3.0.0/arsenal/R/mockstudy.R | 2 arsenal-3.0.0/arsenal/R/modelsum.R | 83 +++---- arsenal-3.0.0/arsenal/R/modelsum.control.R | 2 arsenal-3.0.0/arsenal/R/paired.R | 6 arsenal-3.0.0/arsenal/R/summary.comparedf.R |only arsenal-3.0.0/arsenal/R/summary.freqlist.R | 7 arsenal-3.0.0/arsenal/R/tableby.R | 8 arsenal-3.0.0/arsenal/R/tableby.internal.R | 23 +- arsenal-3.0.0/arsenal/R/tableby.stat.tests.R | 5 arsenal-3.0.0/arsenal/R/tableby.stats.R | 19 - arsenal-3.0.0/arsenal/R/write2.R | 4 arsenal-3.0.0/arsenal/README.md | 20 - arsenal-3.0.0/arsenal/build/vignette.rds |binary arsenal-3.0.0/arsenal/inst/doc/comparedf.R |only arsenal-3.0.0/arsenal/inst/doc/comparedf.Rmd |only arsenal-3.0.0/arsenal/inst/doc/comparedf.html |only arsenal-3.0.0/arsenal/inst/doc/freqlist.R | 3 arsenal-3.0.0/arsenal/inst/doc/freqlist.Rmd | 9 arsenal-3.0.0/arsenal/inst/doc/freqlist.html | 21 + arsenal-3.0.0/arsenal/inst/doc/labels.R | 5 arsenal-3.0.0/arsenal/inst/doc/labels.Rmd | 8 arsenal-3.0.0/arsenal/inst/doc/labels.html | 11 arsenal-3.0.0/arsenal/inst/doc/modelsum.html | 4 arsenal-3.0.0/arsenal/inst/doc/paired.html | 2 arsenal-3.0.0/arsenal/inst/doc/tableby.R | 19 - arsenal-3.0.0/arsenal/inst/doc/tableby.Rmd | 26 +- arsenal-3.0.0/arsenal/inst/doc/tableby.html | 56 +++-- arsenal-3.0.0/arsenal/inst/doc/write2.Rmd | 6 arsenal-3.0.0/arsenal/inst/doc/write2.html | 10 arsenal-3.0.0/arsenal/man/arsenal-defunct.Rd |only arsenal-3.0.0/arsenal/man/arsenal-deprecated.Rd |only arsenal-3.0.0/arsenal/man/arsenal.Rd | 2 arsenal-3.0.0/arsenal/man/comparedf.Rd |only arsenal-3.0.0/arsenal/man/comparedf.control.Rd |only arsenal-3.0.0/arsenal/man/comparedf.tolerances.Rd |only arsenal-3.0.0/arsenal/man/diffs.Rd | 33 +- arsenal-3.0.0/arsenal/man/formulize.Rd | 14 + arsenal-3.0.0/arsenal/man/freq.control.Rd | 2 arsenal-3.0.0/arsenal/man/freqlist.Rd | 8 arsenal-3.0.0/arsenal/man/freqlist.internal.Rd | 23 +- arsenal-3.0.0/arsenal/man/keep.labels.Rd | 21 + arsenal-3.0.0/arsenal/man/mockstudy.Rd | 2 arsenal-3.0.0/arsenal/man/modelsum.Rd | 3 arsenal-3.0.0/arsenal/man/modelsum.control.Rd | 2 arsenal-3.0.0/arsenal/man/reexports.Rd | 2 arsenal-3.0.0/arsenal/man/summary.compare.Rd | 22 - arsenal-3.0.0/arsenal/man/summary.freqlist.Rd | 3 arsenal-3.0.0/arsenal/man/tableby.Rd | 2 arsenal-3.0.0/arsenal/man/tableby.internal.Rd | 5 arsenal-3.0.0/arsenal/man/write2.Rd | 9 arsenal-3.0.0/arsenal/tests/testthat/helper-data.R | 50 ++-- arsenal-3.0.0/arsenal/tests/testthat/mdat.rds |only arsenal-3.0.0/arsenal/tests/testthat/test_comparedf.R |only arsenal-3.0.0/arsenal/tests/testthat/test_formulize.R | 100 +++++--- arsenal-3.0.0/arsenal/tests/testthat/test_freqlist.R | 48 ++++ arsenal-3.0.0/arsenal/tests/testthat/test_keep.labels.R | 8 arsenal-3.0.0/arsenal/tests/testthat/test_lhs_freqlist.R | 168 +++++++++++++-- arsenal-3.0.0/arsenal/tests/testthat/test_lhs_tableby.R | 28 ++ arsenal-3.0.0/arsenal/tests/testthat/test_modelsum.R | 55 ++++ arsenal-3.0.0/arsenal/tests/testthat/test_tableby.R | 49 +++- arsenal-3.0.0/arsenal/vignettes/comparedf.Rmd |only arsenal-3.0.0/arsenal/vignettes/freqlist.Rmd | 9 arsenal-3.0.0/arsenal/vignettes/labels.Rmd | 8 arsenal-3.0.0/arsenal/vignettes/tableby.Rmd | 26 +- arsenal-3.0.0/arsenal/vignettes/write2.Rmd | 6 97 files changed, 1099 insertions(+), 412 deletions(-)
Title: Arrange 'Grobs' in Tables
Description: Tools to make it easier to work with "tables" of
'grobs'. The 'gtable' package defines a 'gtable' grob class that specifies a
grid along with a list of grobs and their placement in the grid. Further the
package makes it easy to manipulate and combine 'gtable' objects so that
complex compositions can be build up sequentially.
Author: Hadley Wickham [aut, cre],
Thomas Lin Pedersen [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between gtable versions 0.2.0 dated 2016-02-26 and 0.3.0 dated 2019-03-25
gtable-0.2.0/gtable/man/z_arrange_gtables.Rd |only gtable-0.2.0/gtable/man/z_normalise.Rd |only gtable-0.3.0/gtable/DESCRIPTION | 47 ++++- gtable-0.3.0/gtable/MD5 | 94 ++++++----- gtable-0.3.0/gtable/NEWS.md | 24 ++ gtable-0.3.0/gtable/R/add-grob.r | 99 ++++++++--- gtable-0.3.0/gtable/R/add-rows-cols.r | 61 +++++-- gtable-0.3.0/gtable/R/add-space.r | 52 ++++-- gtable-0.3.0/gtable/R/align.r | 54 +++--- gtable-0.3.0/gtable/R/filter.r | 25 ++ gtable-0.3.0/gtable/R/grid.r | 48 +++-- gtable-0.3.0/gtable/R/gtable-layouts.r | 108 ++++++++---- gtable-0.3.0/gtable/R/gtable-package.R |only gtable-0.3.0/gtable/R/gtable.r | 126 ++++++++------ gtable-0.3.0/gtable/R/new-data-frame.r |only gtable-0.3.0/gtable/R/padding.r | 12 + gtable-0.3.0/gtable/R/rbind-cbind.r | 98 +++++++++-- gtable-0.3.0/gtable/R/trim.r | 31 ++- gtable-0.3.0/gtable/R/utils.r | 30 ++- gtable-0.3.0/gtable/R/z.r | 14 + gtable-0.3.0/gtable/README.md | 127 ++++++++++++++- gtable-0.3.0/gtable/build |only gtable-0.3.0/gtable/inst |only gtable-0.3.0/gtable/man/bind.Rd | 39 ++++ gtable-0.3.0/gtable/man/figures |only gtable-0.3.0/gtable/man/gtable-package.Rd |only gtable-0.3.0/gtable/man/gtable.Rd | 39 ++-- gtable-0.3.0/gtable/man/gtable_add_cols.Rd | 24 ++ gtable-0.3.0/gtable/man/gtable_add_grob.Rd | 39 +++- gtable-0.3.0/gtable/man/gtable_add_padding.Rd | 17 +- gtable-0.3.0/gtable/man/gtable_add_rows.Rd | 20 ++ gtable-0.3.0/gtable/man/gtable_add_space.Rd | 34 +++- gtable-0.3.0/gtable/man/gtable_col.Rd | 20 +- gtable-0.3.0/gtable/man/gtable_filter.Rd | 28 ++- gtable-0.3.0/gtable/man/gtable_height.Rd | 1 gtable-0.3.0/gtable/man/gtable_matrix.Rd | 18 +- gtable-0.3.0/gtable/man/gtable_row.Rd | 18 +- gtable-0.3.0/gtable/man/gtable_show_layout.Rd | 29 +++ gtable-0.3.0/gtable/man/gtable_spacer.Rd | 17 +- gtable-0.3.0/gtable/man/gtable_trim.Rd | 9 - gtable-0.3.0/gtable/man/gtable_width.Rd | 1 gtable-0.3.0/gtable/man/is.gtable.Rd | 1 gtable-0.3.0/gtable/man/print.gtable.Rd | 1 gtable-0.3.0/gtable/tests/testthat/Rplots.pdf |binary gtable-0.3.0/gtable/tests/testthat/test-bind.r | 6 gtable-0.3.0/gtable/tests/testthat/test-filter.R |only gtable-0.3.0/gtable/tests/testthat/test-layout.r | 50 +++-- gtable-0.3.0/gtable/tests/testthat/test-new-data-frame.R |only gtable-0.3.0/gtable/tests/testthat/test-subsetting.r | 68 ++++---- gtable-0.3.0/gtable/tests/testthat/test-trim.R |only gtable-0.3.0/gtable/tests/testthat/test-z-order.r | 18 +- gtable-0.3.0/gtable/vignettes |only 52 files changed, 1111 insertions(+), 436 deletions(-)
Title: Epimed Solutions Collection for Data Editing, Analysis, and
Benchmark of Health Units
Description: Collection of functions for data analysis and
editing of clinical and epidemiological data.
Most of them are related to benchmark with prediction models.
Author: Lunna Borges [aut, cre],
Pedro Brasil [aut],
Camila Cardoso [aut],
Caio Ferreira [aut]
Maintainer: Lunna Borges <lunna.borges@epimedsolutions.com>
Diff between ems versions 1.2.6 dated 2019-03-12 and 1.2.7 dated 2019-03-25
DESCRIPTION | 12 ++--- MD5 | 6 +- NEWS | 7 +++ R/mortality_rate.R | 116 +++++++++++++++++++++++++++-------------------------- 4 files changed, 76 insertions(+), 65 deletions(-)
Title: Create Tables for Reporting Clinical Trials
Description: Create Tables for Reporting Clinical Trials.
Calculates descriptive statistics and hypothesis tests,
arranges the results in a table ready for reporting with LaTeX, HTML or Word.
Author: Armin Ströbel [aut, cre]
Maintainer: Armin Ströbel <armin-michael.stroebel@dzne.de>
Diff between atable versions 0.1.0 dated 2018-09-13 and 0.1.1 dated 2019-03-25
DESCRIPTION | 16 ++-- MD5 | 75 +++++++++++----------- NAMESPACE | 2 R/atable.R | 110 +++++++++++++++++++++++++-------- R/atable_options.R | 55 +++++++++++++++- R/atable_options_reset.R | 4 - R/check_format_statistics.R | 10 --- R/check_format_tests.R | 9 -- R/check_statistics.R | 10 +-- R/check_tests.R | 10 +-- R/format_statistics.R | 83 ++++++++++++++---------- R/format_tests.R | 29 +++++++- R/helper.R | 87 ++++++++++++++------------ R/indent_data_frame.R | 14 +--- R/multi_sample_htest.R | 44 ++++++++++++- R/standardized_test_data.R | 2 R/statistics.R | 50 ++++++++++++--- R/test_data.R | 2 R/two_sample_htest.R | 54 +++++++++++++--- build/vignette.rds |binary inst/doc/atable_usage.R | 47 ++++++++------ inst/doc/atable_usage.pdf |binary inst/doc/atable_usage.rnw | 77 ++++++++++++++--------- man/atable.Rd | 74 ++++++++++++++++++++-- man/atable_options.Rd | 40 ++++++++++++ man/atable_options_reset.Rd | 4 - man/format_statistics.Rd | 13 +++ man/format_tests.Rd | 18 ++++- man/indent_data_frame.Rd | 2 man/multi_sample_htest.Rd | 19 ++++- man/standardized_test_data.Rd | 2 man/statistics.Rd | 28 ++++++-- man/test_data.Rd | 2 man/two_sample_htest.Rd | 27 ++++++-- tests/testthat/test_atable.R | 5 + tests/testthat/test_atable_Options.R | 2 tests/testthat/test_modify_atable.R |only vignettes/atable_usage-concordance.tex | 4 - vignettes/atable_usage.rnw | 77 ++++++++++++++--------- 39 files changed, 783 insertions(+), 324 deletions(-)
Title: Turner Miscellaneous
Description: Miscellaneous utility functions for data manipulation,
data tidying, and working with gene expression data.
Author: Stephen Turner [aut, cre] (<https://orcid.org/0000-0001-9140-9028>)
Maintainer: Stephen Turner <vustephen@gmail.com>
Diff between Tmisc versions 0.1.19 dated 2018-03-20 and 0.1.20 dated 2019-03-25
Tmisc-0.1.19/Tmisc/R/datename.R |only Tmisc-0.1.19/Tmisc/R/registration.R |only Tmisc-0.1.19/Tmisc/man/datename.Rd |only Tmisc-0.1.19/Tmisc/man/registration.Rd |only Tmisc-0.1.20/Tmisc/DESCRIPTION | 8 - Tmisc-0.1.20/Tmisc/MD5 | 30 +++---- Tmisc-0.1.20/Tmisc/NAMESPACE | 2 Tmisc-0.1.20/Tmisc/NEWS.md | 5 + Tmisc-0.1.20/Tmisc/R/deseqresult2tbl.R | 1 Tmisc-0.1.20/Tmisc/R/dfsigfig.R | 3 Tmisc-0.1.20/Tmisc/R/keep_top_n.R | 3 Tmisc-0.1.20/Tmisc/R/rownames_to_symprobe.R | 1 Tmisc-0.1.20/Tmisc/R/unfactor.R | 5 - Tmisc-0.1.20/Tmisc/inst/rmarkdown/templates/Tmisc/skeleton/skeleton.Rmd | 41 +++------- Tmisc-0.1.20/Tmisc/man/dfsigfig.Rd | 2 Tmisc-0.1.20/Tmisc/man/keep_top_n.Rd | 2 Tmisc-0.1.20/Tmisc/man/lsa.Rd | 4 Tmisc-0.1.20/Tmisc/man/unfactor.Rd | 2 18 files changed, 55 insertions(+), 54 deletions(-)
Title: Interface to the 'g:Profiler' Toolset
Description: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler>).
The main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects
This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Author: Liis Kolberg <liis.kolberg@ut.ee>, Uku Raudvere <uku.raudvere@ut.ee>
Maintainer: Liis Kolberg <liis.kolberg@ut.ee>
Diff between gprofiler2 versions 0.1.0 dated 2019-03-06 and 0.1.1 dated 2019-03-25
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/gprofiler2.R | 4 ++-- README.md | 5 +++++ man/gost.Rd | 4 ++-- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: A Parallel Clustering Non-Uniform Memory Access ('NUMA')
Optimized Package
Description: The clustering 'NUMA' Optimized Routines package or 'clusternor' is a highly optimized package for performing clustering in parallel with accelerations specifically targeting multi-core Non-Uniform Memory Access ('NUMA') hardware architectures. Disa Mhembere, Da Zheng, Carey E. Priebe, Joshua T. Vogelstein, Randal Burns (2019) <arXiv:1902.09527>.
Author: Disa Mhembere [aut, cre],
Neurodata (https://neurodata.io) [cph]
Maintainer: Disa Mhembere <disa@cs.jhu.edu>
Diff between clusternor versions 0.0-1 dated 2019-03-18 and 0.0-2 dated 2019-03-25
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/cknor/libman/coordinator.hpp | 2 +- src/cknor/libman/kmeans_task_coordinator.cpp | 26 ++++++++++++++++++++------ src/cknor/libman/medoid.hpp | 4 ++-- src/rinterface.cpp | 1 + 6 files changed, 33 insertions(+), 18 deletions(-)
Title: Spatial Graph Based Clustering Summaries for Spatial Point
Patterns
Description: Graph based clustering summaries for spatial point patterns.
Includes Connectivity function, Cumulative connectivity function and clustering
function, plus the triangle/triplet intensity function T.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>
Diff between SGCS versions 2.6 dated 2017-04-18 and 2.7 dated 2019-03-25
DESCRIPTION | 10 +++++----- MD5 | 44 ++++++++++++++++++++++---------------------- NAMESPACE | 2 +- man/Kfun.Rd | 1 - man/Rfun.Rd | 1 - man/SGCS.Rd | 1 - man/Tfun.Rd | 1 - man/arcs.Rd | 1 - man/bounding_box_xy.Rd | 1 - man/clustfun.Rd | 1 - man/clustfun_denominator.Rd | 1 - man/confun.Rd | 1 - man/default_r.Rd | 1 - man/edge_distance.Rd | 1 - man/internal_to_ppp.Rd | 1 - man/internalise_pp.Rd | 1 - man/morphoArea.Rd | 1 - man/morphoEuler.Rd | 1 - man/morphoLength.Rd | 1 - man/pairwise_distances.Rd | 1 - man/translation_weights.Rd | 1 - src/Components.cpp | 2 +- src/Rextras.cpp | 2 +- 23 files changed, 30 insertions(+), 48 deletions(-)
Title: Efficient Design and Analysis of Cluster Randomized Trials
Description: Constrained randomization by Raab and Butcher (2001) <doi:10.1002/1097-0258(20010215)20:3%3C351::AID-SIM797%3E3.0.CO;2-C>
is suitable for cluster randomized trials (CRTs) with a
small number of clusters (e.g., 20 or fewer). The procedure of
constrained randomization is based on the baseline values of some
cluster-level covariates specified. The intervention effect on
the individual outcome can then be analyzed through
clustered permutation test introduced by Gail, et al. (1996) <doi:10.1002/(SICI)1097-0258(19960615)15:11%3C1069::AID-SIM220%3E3.0.CO;2-Q>.
Motivated from Li, et al. (2016) <doi:10.1002/sim.7410>, the package performs constrained randomization on the baseline
values of cluster-level covariates and cluster permutation test on the individual-level outcome for cluster randomized trials.
Author: Hengshi Yu [aut, cre],
Fan Li [aut],
John A. Gallis [aut],
Elizabeth L. Turner [aut]
Maintainer: Hengshi Yu <hengshi@umich.edu>
Diff between cvcrand versions 0.0.3 dated 2019-02-27 and 0.0.4 dated 2019-03-25
cvcrand-0.0.3/cvcrand/inst/dickinson_bscores.csv |only cvcrand-0.0.4/cvcrand/DESCRIPTION | 8 cvcrand-0.0.4/cvcrand/MD5 | 31 cvcrand-0.0.4/cvcrand/NAMESPACE | 1 cvcrand-0.0.4/cvcrand/NEWS.md | 11 cvcrand-0.0.4/cvcrand/R/cptest.R | 22 cvcrand-0.0.4/cvcrand/R/cvcrand_package.R | 24 cvcrand-0.0.4/cvcrand/R/cvrall.R | 1732 +++++++++++------------ cvcrand-0.0.4/cvcrand/R/cvrcov.R | 79 - cvcrand-0.0.4/cvcrand/inst/doc/cvcrand.R | 4 cvcrand-0.0.4/cvcrand/inst/doc/cvcrand.Rmd | 28 cvcrand-0.0.4/cvcrand/inst/doc/cvcrand.html | 110 - cvcrand-0.0.4/cvcrand/man/cptest.Rd | 5 cvcrand-0.0.4/cvcrand/man/cvrall.Rd | 29 cvcrand-0.0.4/cvcrand/man/cvrcov.Rd | 9 cvcrand-0.0.4/cvcrand/vignettes/cvcrand.Rmd | 28 cvcrand-0.0.4/cvcrand/vignettes/references.bib | 21 17 files changed, 1080 insertions(+), 1062 deletions(-)
Title: Advanced Data Analysis of Immune Receptor Repertoires
Description: Platform for the advanced analysis of T cell receptor and
Immunoglobulin repertoires data and visualisation of the analysis results.
Author: Vadim Nazarov
Maintainer: Vadim Nazarov <vdm.nazarov@gmail.com>
Diff between tcR versions 2.2.3 dated 2019-01-07 and 2.2.4 dated 2019-03-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/onload.R | 18 ++++++++++-------- README.md | 10 +++++++++- inst/doc/tcrvignette.html | 6 +++--- 5 files changed, 30 insertions(+), 20 deletions(-)
Title: Portfolio Safeguard: Optimization, Statistics and Risk
Management
Description: Solves optimization, advanced statistics, and risk management problems. Popular nonlinear functions in financial, statistical, and logistics applications are pre-coded (e.g., Standard Deviation, Entropy, Expected Shortfall (ES), Value-at-Risk (VaR), Conditional Value-at-Risk (CVaR), Probability of Exceedance (POE), Buffered Probability of Exceedance (bPOE), Partial Moment (PM), Drawdown, Mean-Squared Error, see, the list <http://www.aorda.com/html/PSG_Help_HTML/index.html?function.htm> ). 'PSGExpress' is the 'Portfolio Safeguard (PSG)' freeware version with the number of variables in functions less or equal to 10, see <http://www.aorda.com>.
Author: Stan Uryasev [aut, cre, cph],
Grigoriy Zrazhevsky [aut],
Viktor Kuzmenko [aut],
Alex Zrazhevsky [aut]
Maintainer: Stan Uryasev <stan.uryasev@aorda.com>
Diff between PSGExpress versions 3.1.1 dated 2019-03-21 and 3.1.2 dated 2019-03-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/partial.rdb |binary src/Makevars | 8 +++++--- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC; Dimitris Rizopoulos (2016) <doi:10.18637/jss.v072.i07>.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes versions 0.8-82 dated 2019-03-20 and 0.8-83 dated 2019-03-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/JMbayes.Rd | 4 ++-- src/fast_LAPRWM.cpp | 12 ++++++------ 4 files changed, 15 insertions(+), 15 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 0.3.9 dated 2019-01-02 and 0.4.0 dated 2019-03-25
DESCRIPTION | 6 MD5 | 76 +- NEWS | 25 NEWS.md | 25 R/aggregate.R | 370 +++++----- R/datesManipulations.R | 942 ++++++++++++++-------------- R/discretization.R | 471 +++++++------- R/generateFromCharacter.R | 162 ++-- R/generateFromFactor.R | 502 +++++++------- R/genericFunctions.R | 828 ++++++++++++------------ R/sameShape.R | 301 ++++---- R/setColAs.R | 778 +++++++++++------------ R/shapeSet.R | 256 +++---- R/whichFunctions.R | 725 ++++++++++----------- build/vignette.rds |binary inst/doc/dataPreparation.html | 53 - inst/doc/train_test_prep.html | 19 man/aggregateByKey.Rd | 6 man/generateFromCharacter.Rd | 3 man/generateFromFactor.Rd | 3 man/whichAreIncluded.Rd | 5 tests/testthat/test_aggregate.R | 211 ++++-- tests/testthat/test_datesManipulation.R | 479 +++++++++----- tests/testthat/test_description.R | 50 - tests/testthat/test_discretization.R | 316 +++++++-- tests/testthat/test_factorManipulation.R | 78 +- tests/testthat/test_fastFunctions.R | 434 +++++++++--- tests/testthat/test_fast_posixct.R | 25 tests/testthat/test_generateFromCharacter.R | 58 - tests/testthat/test_generateFromDate.R | 293 ++++++-- tests/testthat/test_generateFromFactor.R | 147 ++-- tests/testthat/test_genericFunctions.R | 610 +++++++++++++++--- tests/testthat/test_numericsManipulations.R | 177 +++-- tests/testthat/test_prepareSet.R | 37 - tests/testthat/test_sameShape.R | 208 ++++-- tests/testthat/test_scale.R | 222 ++++-- tests/testthat/test_setColAs.R | 402 ++++++++--- tests/testthat/test_shapeSet.R | 152 +++- tests/testthat/test_whichFunctions.R | 296 ++++++-- 39 files changed, 5938 insertions(+), 3813 deletions(-)
More information about dataPreparation at CRAN
Permanent link
Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso' as described by Schauberger and Tutz (2019) <doi:10.18637/jss.v088.i09> and Schauberger and Tutz (2017) <doi:10.1177/1471082X17693086>. BTLLasso is a method to include different types of variables in paired comparison models and, therefore, to allow for heterogeneity between subjects. Variables can be subject-specific, object-specific and subject-object-specific and can have an influence on the attractiveness/strength of the objects. Suitable L1 penalty terms are used to cluster certain effects and to reduce the complexity of the models.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between BTLLasso versions 0.1-9 dated 2019-03-06 and 0.1-10 dated 2019-03-25
DESCRIPTION | 10 ++++---- MD5 | 51 ++++++++++++++++++++++----------------------- R/BTLLasso-package.R | 2 - R/BTLLasso.R | 2 - R/boot.BTLLasso.R | 2 - R/cv.BTLLasso.R | 2 - R/paths.R | 2 - R/plot.BTLLasso.R | 2 - R/plot.boot.BTLLasso.R | 2 - R/predict.BTLLasso.R | 2 - R/print.BTLLasso.R | 2 - R/print.boot.BTLLasso.R | 2 - R/print.cv.BTLLasso.R | 2 - R/response.BTLLasso.R | 2 - inst |only man/BTLLasso-package.Rd | 2 - man/boot.BTLLasso.Rd | 2 - man/ctrl.BTLLasso.Rd | 2 - man/cv.BTLLasso.Rd | 2 - man/paths.Rd | 2 - man/plot.BTLLasso.Rd | 2 - man/plot.boot.BTLLasso.Rd | 2 - man/predict.BTLLasso.Rd | 2 - man/print.BTLLasso.Rd | 2 - man/print.boot.BTLLasso.Rd | 2 - man/print.cv.BTLLasso.Rd | 2 - man/response.BTLLasso.Rd | 2 - 27 files changed, 55 insertions(+), 54 deletions(-)
Title: Dynamics of Return to Equilibrium During Multiple Inputs
Description: Provides models to fit the dynamics of a regulated
system experiencing exogenous inputs. The underlying models use differential
equations and linear mixed-effects regressions to estimate the characteristic
parameters of the equation (the coefficients) and an estimated signal. The
package also provides print, summary, plot and predict functions, specific for
the models outputs.
Author: Mongin Denis [aut],
Uribe Adriana [aut],
Courvoisier Delphine [aut],
Courvoisier Delphine [cre]
Maintainer: Courvoisier Delphine <Delphine.Courvoisier@hcuge.ch>
Diff between doremi versions 0.1.0 dated 2018-08-30 and 0.1.1 dated 2019-03-25
DESCRIPTION | 6 MD5 | 17 +- NEWS.md |only R/doremi.R | 100 +++++++++----- R/others.R | 15 +- build/vignette.rds |binary inst/doc/Introduction-to-doremi.R | 5 inst/doc/Introduction-to-doremi.Rmd | 9 - inst/doc/Introduction-to-doremi.html | 234 +++++++++++++++++------------------ vignettes/Introduction-to-doremi.Rmd | 9 - 10 files changed, 213 insertions(+), 182 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-25 1.0.0
Title: Cost Constrained Flux Balance Analysis (ccFBA): MetabOlic
Modeling with ENzyme kineTics (MOMENT)
Description: Different techniques of cost constrained flux balance analysis.
1- MetabOlic Modeling with ENzyme kineTics 'MOMENT' which uses enzyme kinetic data and enzyme molecular
weights to constrain flux balance analysis(FBA) and it is described in Adadi, R., Volkmer, B., Milo, R.,
Heinemann, M., & Shlomi, T. (2012). Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network
with Kinetic Parameters, 8(7). <doi:10.1371/journal.pcbi.1002575>.
2- an improvement of 'MOMENT' that considers multi-functional enzymes 'ccFBA'.
Described in Desouki, Abdelmoneim. Algorithms for improving the predictive power of flux balance analysis. PhD dissertation, 2016.
FBA is a mathematical technique to find fluxes in metabolic models at steady state.
It is described in Orth, J.D., Thiele, I. and Palsson, B.O. What is flux balance analysis? Nat. Biotech. 28, 245-248(2010).
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki <abdelmoneim.amer@uni-duesseldorf.de>
Diff between sybilccFBA versions 2.0.0 dated 2015-04-02 and 3.0.0 dated 2019-03-25
DESCRIPTION | 37 +- MD5 | 59 ++- NAMESPACE | 4 NEWS | 28 + R/calc_MW.R | 34 +- R/cfba_moment.R | 263 +++++++++++++-- R/cfba_moment_mr.R | 582 ++++++++++++++++++++++++++--------- R/getGpr1iso.R |only R/getRevFlux.R | 10 R/getccFBA_mat.R |only R/simulate_EColi.R |only R/sysBiolAlg_ccFBAClass.R |only data/iAF1260.RData |binary data/iJO1366.RData |binary data/iML1515.RData |only data/iMM904.RData |binary data/kcat.RData |binary data/mw.RData |binary data/mw_iML1515.RData |only data/yst_kcat.RData |binary data/yst_mw.RData |binary inst/extdata/Ec_core_genedef.csv |only inst/extdata/Ec_iAF1260_genedef.csv |only inst/extdata/allKcats_upd34_dd_h.csv |only inst/extdata/cpx_stoich_me.csv |only inst/extdata/iJO1366_genedef.csv |only inst/extdata/yst_genedef.csv |only man/addGlcTrns.Rd | 2 man/cfba_moment.Rd | 103 +++++- man/cfba_moment_mr.Rd | 36 +- man/getGpr1iso.Rd |only man/getRevFlux.Rd | 63 --- man/getccFBA_mat.Rd |only man/iML1515.Rd |only man/initialize-methods.Rd |only man/mw_iML1515.Rd |only man/readmodel.Rd | 94 ----- man/simulate_EColi.Rd |only man/sybilccFBA-package.Rd | 159 +++++++++ man/sysBiolAlg_ccFBA-class.Rd |only 40 files changed, 1074 insertions(+), 400 deletions(-)
Title: Directional Statistics
Description: A collection of functions for directional data analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 3.4 dated 2018-11-12 and 3.6 dated 2019-03-25
DESCRIPTION | 13 +++++++------ MD5 | 35 +++++++++++++++++++++-------------- NAMESPACE | 7 ++++--- R/ESAGmle.R | 2 +- R/circ.cor1.R | 17 +---------------- R/circ.cors1.R |only R/dirda.cv.R | 6 +++--- R/dirknn.R | 4 ++-- R/dirknn.tune.R | 4 ++-- R/kent.density.R | 6 +++--- R/purka.mle.R |only R/vm.density.R |only R/vmf.density.R |only man/Directional-package.Rd | 10 +++++++--- man/circ.cors1.Rd |only man/dirda.cv.Rd | 10 +++++++--- man/dirknn.Rd | 5 ++++- man/dirknn.tune.Rd | 43 +++++++++++++++++++++++-------------------- man/ggvm.Rd | 2 +- man/kent.density.Rd | 19 ++++++++++++------- man/purka.mle.Rd |only man/vm.density.Rd |only 22 files changed, 98 insertions(+), 85 deletions(-)
Title: Wrapper for the Gnu Scientific Library
Description: An R wrapper for some of the functionality of the
Gnu Scientific Library.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>),
Andrew Clausen [ctb] (multimin functionality),
Duncan Murdoch [ctb] (qrng functions)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between gsl versions 2.1-5 dated 2019-03-15 and 2.1-6 dated 2019-03-25
DESCRIPTION | 6 - MD5 | 21 +-- NAMESPACE | 276 +++++++++++++++++++++++++++++++++++++++++++++++++- R/error.R | 4 R/multimin.R | 268 ++++++++++++++++++++++++------------------------ build/partial.rdb |binary inst/doc/gslpaper.pdf |binary man/Error.Rd | 2 src/error.c | 6 - src/init.c |only src/qrng.c | 6 - src/rng.c | 3 12 files changed, 434 insertions(+), 158 deletions(-)
Title: Cognitive Models
Description: Hierarchical Bayesian models. The package provides tools to fit two popular response time models, using population-based Markov Chain Monte Carlo (pMCMC). The paper by Heathcote, Lin, Reynolds, Strickland, Gretton, and Matzke (2018, <doi:10.3758/s13428-018-1067-y>) describes the prototype of the package.
Author: Yi-Shin Lin [aut, cre], Andrew Heathcote [aut]
Maintainer: Yi-Shin Lin <yishinlin001@gmail.com>
Diff between ggdmc versions 0.2.5.6 dated 2019-03-22 and 0.2.5.7 dated 2019-03-25
ggdmc-0.2.5.6/ggdmc/src/Makevars |only ggdmc-0.2.5.7/ggdmc/DESCRIPTION | 8 ggdmc-0.2.5.7/ggdmc/MD5 | 16 - ggdmc-0.2.5.7/ggdmc/README.md | 123 +++------- ggdmc-0.2.5.7/ggdmc/cleanup |only ggdmc-0.2.5.7/ggdmc/configure |only ggdmc-0.2.5.7/ggdmc/configure.ac |only ggdmc-0.2.5.7/ggdmc/inst/include/RcppArmadilloConfigGenerated.h.in |only ggdmc-0.2.5.7/ggdmc/inst/include/ggdmc/Likelihood.hpp | 2 ggdmc-0.2.5.7/ggdmc/src/FCalculator.cpp | 2 ggdmc-0.2.5.7/ggdmc/src/Makevars.in |only ggdmc-0.2.5.7/ggdmc/src/Makevars.win | 17 - 12 files changed, 63 insertions(+), 105 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-06-28 0.0.1
2016-05-03 0.0.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-21 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-16 0.0.19
2017-12-20 0.0.18
2017-09-08 0.0.17
2017-01-14 0.0.16
2017-01-09 0.0.15
2016-12-16 0.0.14
2016-10-26 0.0.13
2015-11-05 0.0.12
2015-08-26 0.0.11
2015-06-16 0.0.10
2015-01-08 0.0.8
2014-12-09 0.0.7
2014-09-04 0.0.6
2013-12-11 0.0.3
2013-11-29 0.0.1
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the
location of the species is needed and about the environmental conditions. To test
for significance habitat associations, one of the two components is randomized.
Methods are mainly based on Plotkin et al. (2000) <doi:10.1006/jtbi.2000.2158> and
Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>)
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between shar versions 0.2 dated 2019-02-06 and 0.3 dated 2019-03-25
shar-0.2/shar/R/shar.R |only shar-0.2/shar/vignettes/methods.png |only shar-0.3/shar/DESCRIPTION | 11 shar-0.3/shar/MD5 | 87 ++- shar-0.3/shar/NAMESPACE | 4 shar-0.3/shar/NEWS.md | 21 shar-0.3/shar/R/RcppExports.R |only shar-0.3/shar/R/SHAR.R |only shar-0.3/shar/R/calculate_energy.R | 185 +++++-- shar-0.3/shar/R/estimate_pcf_fast.R | 86 +-- shar-0.3/shar/R/fit_point_process.R | 17 shar-0.3/shar/R/onUnload.R |only shar-0.3/shar/R/plot_randomized_pattern.R | 237 ++++++---- shar-0.3/shar/R/plot_randomized_raster.R |only shar-0.3/shar/R/randomize_raster.R | 12 shar-0.3/shar/R/reconstruct_marks.R | 73 +-- shar-0.3/shar/R/reconstruct_pattern.R | 216 +++++---- shar-0.3/shar/R/results_habitat_association.R | 2 shar-0.3/shar/build/vignette.rds |binary shar-0.3/shar/inst/doc/background.R |only shar-0.3/shar/inst/doc/background.Rmd | 32 + shar-0.3/shar/inst/doc/background.html | 30 - shar-0.3/shar/inst/doc/publication_record.Rmd | 2 shar-0.3/shar/inst/doc/publication_record.html | 7 shar-0.3/shar/inst/doc/reconstruct_multiple_patterns.R |only shar-0.3/shar/inst/doc/reconstruct_multiple_patterns.Rmd |only shar-0.3/shar/inst/doc/reconstruct_multiple_patterns.html |only shar-0.3/shar/man/calculate_energy.Rd | 16 shar-0.3/shar/man/figures/README-plot-1.png |only shar-0.3/shar/man/figures/README-plot-random_pattern-1.png |only shar-0.3/shar/man/figures/README-plot-random_pattern-2.png |only shar-0.3/shar/man/figures/README-plot_habitat-random-1.png |only shar-0.3/shar/man/figures/README-plot_habitat_random-1.png |binary shar-0.3/shar/man/figures/README-plot_random_pattern-1.png |binary shar-0.3/shar/man/figures/README-plot_random_pattern-2.png |only shar-0.3/shar/man/plot_randomized_pattern.Rd | 11 shar-0.3/shar/man/plot_randomized_raster.Rd |only shar-0.3/shar/man/rcpp_sample.Rd |only shar-0.3/shar/man/reconstruct_marks.Rd | 2 shar-0.3/shar/man/shar.Rd |only shar-0.3/shar/src |only shar-0.3/shar/tests/testthat/test-calculate_energy.R | 2 shar-0.3/shar/tests/testthat/test-fit-point_process.R | 6 shar-0.3/shar/tests/testthat/test-plot_randomized_pattern.R | 8 shar-0.3/shar/tests/testthat/test-randomize_raster.R | 6 shar-0.3/shar/tests/testthat/test-reconstruct_marks.R | 40 + shar-0.3/shar/tests/testthat/test-reconstruct_pattern.R | 21 shar-0.3/shar/tests/testthat/test-results_habitat_association.R | 3 shar-0.3/shar/vignettes/background.Rmd | 32 + shar-0.3/shar/vignettes/gamma_vs_reconstruction.png |only shar-0.3/shar/vignettes/methods_overview.png |only shar-0.3/shar/vignettes/pattern_reconstruction.gif |only shar-0.3/shar/vignettes/publication_record.Rmd | 2 shar-0.3/shar/vignettes/random_walk.gif |only shar-0.3/shar/vignettes/reconstruct_multiple_patterns.Rmd |only 55 files changed, 768 insertions(+), 403 deletions(-)
Title: Explore the Innards of 'ggplot2' Objects
Description: Extensions to 'ggplot2' providing low-level debug tools: statistics
and geometries reporting data passed to compute_group() and compute_panel()
functions and to geometries. Layer manipulation: functions for deletion,
insertion, extraction and reordering of layers of "ggplot" objects. Data
manipulation: function for deletion of unused variables from the
data object embedded in "ggplot" objects.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between gginnards versions 0.0.1 dated 2018-07-13 and 0.0.2 dated 2019-03-25
DESCRIPTION | 20 +- MD5 | 50 +++--- NAMESPACE | 6 NEWS | 10 + R/data-manip.R | 131 ++++++++++++---- R/geom-debug.R | 2 R/gg-structure.R |only R/gginnards.R | 15 - R/layer-manip.R | 12 - R/on-attach.R | 1 README.md | 8 build/vignette.rds |binary inst/doc/user-guide-1.R | 2 inst/doc/user-guide-1.Rmd | 16 - inst/doc/user-guide-1.html | 361 ++++++++++++++++++++++----------------------- inst/doc/user-guide-2.R | 38 ++++ inst/doc/user-guide-2.Rmd | 118 +++++++++++--- inst/doc/user-guide-2.html | 298 +++++++++++++++++++++++++------------ man/delete_layers.Rd | 2 man/drop_vars.Rd | 79 +++++++-- man/geom_debug.Rd | 2 man/gginnards-package.Rd | 24 +- man/stat_debug_group.Rd | 1 man/stat_debug_panel.Rd | 1 man/str.Rd |only vignettes/user-guide-1.Rmd | 16 - vignettes/user-guide-2.Rmd | 118 +++++++++++--- 27 files changed, 867 insertions(+), 464 deletions(-)
Title: Copula Mixed Models for Multivariate Meta-Analysis of Diagnostic
Test Accuracy Studies
Description: The bivariate copula mixed model for meta-analysis of diagnostic test accuracy studies in Nikoloulopoulos (2015) <doi:10.1002/sim.6595>. The vine copula mixed model for meta-analysis of diagnostic test accuracy studies accounting for disease prevalence in Nikoloulopoulos (2017) <doi:10.1177/0962280215596769> and also accounting for non-evaluable subjects in Nikoloulopoulos (2018) <arXiv:1812.03685>. The hybrid vine copula mixed model for meta-analysis of diagnostic test accuracy case-control and cohort studies in Nikoloulopoulos (2018) <doi:10.1177/0962280216682376>. The D-vine copula mixed model for meta-analysis and comparison of two diagnostic tests in Nikoloulopoulos (2018) <doi:10.1177/0962280218796685>. The multinomial quadrivariate D-vine copula mixed model for meta-analysis of diagnostic tests with non-evaluable subjects in Nikoloulopoulos (2018) <arXiv:1812.05915>.
Author: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>
Maintainer: Aristidis K. Nikoloulopoulos <A.Nikoloulopoulos@uea.ac.uk>
Diff between CopulaREMADA versions 1.2 dated 2019-02-08 and 1.3 dated 2019-03-25
DESCRIPTION | 14 +++++++------- INDEX | 6 ++++++ MD5 | 27 +++++++++++++++++---------- NAMESPACE | 7 +++++-- R/MLest-4variate-multinomial-truncated.R |only R/MLest-4variate-multinomial.R |only R/SROC.R | 19 ++++++++++++------- R/dvinesim.R | 10 +++++----- R/simMultinom.R |only build/partial.rdb |binary data/MK2016.rda |only man/CopulaREMADA-package.Rd | 10 ++++++---- man/MK2016.Rd |only man/SROC.Rd | 24 +++++++++++++++++++++--- man/coronary.Rd | 2 +- man/dvinesim.Rd | 21 +++++++++++++-------- man/mutinomVineCopulaREMADA.Rd |only man/rmultinomVineCopulaREMADA.Rd |only 18 files changed, 93 insertions(+), 47 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-24 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-22 0.2.0
2019-02-22 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-23 0.1.0
Title: Tools for Mapping of Quantitative Traits of Genetically Related
Individuals and Calculating Identity Coefficients from
Pedigrees
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng [aut, cre]
Maintainer: Riyan Cheng <riyancheng@hotmail.com>
Diff between QTLRel versions 1.0 dated 2018-01-10 and 1.1 dated 2019-03-25
QTLRel-1.0/QTLRel/src/xxx.h |only QTLRel-1.1/QTLRel/ChangeLog | 1 QTLRel-1.1/QTLRel/DESCRIPTION | 8 QTLRel-1.1/QTLRel/MD5 | 71 + QTLRel-1.1/QTLRel/NAMESPACE | 2 QTLRel-1.1/QTLRel/R/eigen_sym.R |only QTLRel-1.1/QTLRel/R/estVC.R | 760 +++----------------- QTLRel-1.1/QTLRel/R/idcoef.R | 62 + QTLRel-1.1/QTLRel/R/imFn.R | 21 QTLRel-1.1/QTLRel/R/nullSim.R | 10 QTLRel-1.1/QTLRel/R/plots.R | 9 QTLRel-1.1/QTLRel/R/qqPlot.R | 10 QTLRel-1.1/QTLRel/R/scan.R | 933 ++++++++++++++----------- QTLRel-1.1/QTLRel/data/miscEx.RData |binary QTLRel-1.1/QTLRel/inst/doc/QTLRel_Tutorial.R | 28 QTLRel-1.1/QTLRel/inst/doc/QTLRel_Tutorial.pdf |binary QTLRel-1.1/QTLRel/man/cic.Rd | 7 QTLRel-1.1/QTLRel/man/eigen_sym.Rd |only QTLRel-1.1/QTLRel/man/estVC.Rd | 2 QTLRel-1.1/QTLRel/man/genMatrix.Rd | 2 QTLRel-1.1/QTLRel/man/nullSim.Rd | 4 QTLRel-1.1/QTLRel/man/plots.Rd | 2 QTLRel-1.1/QTLRel/man/scanOne.Rd | 36 QTLRel-1.1/QTLRel/src/Makevars |only QTLRel-1.1/QTLRel/src/QTLRelR.c |only QTLRel-1.1/QTLRel/src/QTLRelR.h |only QTLRel-1.1/QTLRel/src/d1mach.c |only QTLRel-1.1/QTLRel/src/distn.c |only QTLRel-1.1/QTLRel/src/dpq.h |only QTLRel-1.1/QTLRel/src/dqrcf.f |only QTLRel-1.1/QTLRel/src/dqrdc2.f |only QTLRel-1.1/QTLRel/src/dqrls.f |only QTLRel-1.1/QTLRel/src/dqrsl.f |only QTLRel-1.1/QTLRel/src/i1mach.c |only QTLRel-1.1/QTLRel/src/ibsFn.c | 2 QTLRel-1.1/QTLRel/src/idcoef.c | 39 - QTLRel-1.1/QTLRel/src/imFn.c | 2 QTLRel-1.1/QTLRel/src/init.c | 21 QTLRel-1.1/QTLRel/src/ks.c | 2 QTLRel-1.1/QTLRel/src/nmath.h |only QTLRel-1.1/QTLRel/src/qqplot.c | 2 QTLRel-1.1/QTLRel/src/rgdat.c | 2 QTLRel-1.1/QTLRel/src/sc10.f |only QTLRel-1.1/QTLRel/src/sc11.f |only QTLRel-1.1/QTLRel/src/sc20.f |only QTLRel-1.1/QTLRel/src/sc21.f |only 46 files changed, 875 insertions(+), 1163 deletions(-)
Title: Copula-Based Estimation and Statistical Process Control for
Serially Correlated Time Series
Description: Estimation and statistical process control are performed under
copula-based time-series models.
Available are statistical methods in Long and Emura (2014 JCSA),
Emura et al. (2017 Commun Stat-Simul) <DOI:10.1080/03610918.2015.1073303>,
Huang and Emura(2019, in revision) and Huang, Chen and Emura (2019-, in revision).
Author: Takeshi Emura, Xinwei Huang, Weiru Chen, Ting-Hsuan Long
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between Copula.Markov versions 2.3 dated 2019-01-15 and 2.4 dated 2019-03-25
DESCRIPTION | 12 MD5 | 34 R/Clayton.Markov.GOF.binom.R |only R/Clayton.Markov.MLE.R | 2 R/Clayton.Markov.MLE.binom.R | 1458 ++++++++++++++++++++------------------- R/Clayton.Markov2.MLE.R | 25 R/Joe.Markov.DATA.binom.R |only R/Joe.Markov.MLE.R | 4 man/Clayton.Markov.DATA.Rd | 4 man/Clayton.Markov.DATA.binom.Rd | 11 man/Clayton.Markov.GOF.Rd | 5 man/Clayton.Markov.GOF.binom.Rd |only man/Clayton.Markov.MLE.Rd | 4 man/Clayton.Markov.MLE.binom.Rd | 15 man/Clayton.Markov2.DATA.Rd | 10 man/Clayton.Markov2.MLE.Rd | 15 man/Copula.Markov-package.Rd | 12 man/Joe.Markov.DATA.Rd | 4 man/Joe.Markov.DATA.binom.Rd |only man/Joe.Markov.MLE.Rd | 4 20 files changed, 875 insertions(+), 744 deletions(-)