Fri, 11 Aug 2017

Package OrgMassSpecR updated to version 0.5-2 with previous version 0.4-6 dated 2016-10-19

Title: Organic Mass Spectrometry
Description: Organic/biological mass spectrometry data analysis.
Author: Nathan Dodder [cre, aut, cph], Katharine Mullen [ctb]
Maintainer: Nathan Dodder <ndodder@mail.sdsu.edu>

Diff between OrgMassSpecR versions 0.4-6 dated 2016-10-19 and 0.5-2 dated 2017-08-11

 DESCRIPTION                         |   12 
 LICENSE                             |    2 
 MD5                                 |   44 -
 NAMESPACE                           |    5 
 R/ListFormula.R                     |    6 
 R/MolecularWeight.R                 |    4 
 R/PeptideSpectrum.R                 |   34 -
 R/ReadMspDirectory.R                |    4 
 R/ReadMspFile.R                     |    4 
 R/SpectrumSimilarity.R              |  149 ++++--
 build/vignette.rds                  |binary
 data/example.sequence.rda           |binary
 inst/NEWS.Rd                        |   42 -
 inst/doc/OrgMassSpecR-examples.R    |    2 
 inst/doc/OrgMassSpecR-examples.Rmd  |   35 -
 inst/doc/OrgMassSpecR-examples.html |  797 ++++++++++++++++++------------------
 man/ListFormula.Rd                  |    5 
 man/MolecularWeight.Rd              |   11 
 man/PeptideSpectrum.Rd              |    1 
 man/ReadMspDirectory.Rd             |    4 
 man/ReadMspFile.Rd                  |    6 
 man/SpectrumSimilarity.Rd           |   26 -
 vignettes/OrgMassSpecR-examples.Rmd |   35 -
 23 files changed, 679 insertions(+), 549 deletions(-)

More information about OrgMassSpecR at CRAN
Permanent link

Package dataMeta updated to version 0.1.1 with previous version 0.1.0 dated 2017-04-24

Title: Create and Append a Data Dictionary for an R Dataset
Description: Designed to create a basic data dictionary and append to the original dataset's attributes list. The package makes use of a tidy dataset and creates a data frame that will serve as a linker that will aid in building the dictionary. The dictionary is then appended to the list of the original dataset's attributes. The user will have the option of entering variable and item descriptions by writing code or use alternate functions that will prompt the user to add these.
Author: Dania M. Rodriguez [aut, cre], P3S Corporation [cph]
Maintainer: Dania M. Rodriguez <dmrodz@gmail.com>

Diff between dataMeta versions 0.1.0 dated 2017-04-24 and 0.1.1 dated 2017-08-11

 DESCRIPTION                     |   14 +++++++++-----
 MD5                             |   11 ++++++-----
 NEWS.md                         |only
 R/build_dict.R                  |   12 +++++++-----
 README.md                       |    6 ++++++
 build/vignette.rds              |binary
 inst/doc/dataMeta_Vignette.html |   10 +++++-----
 7 files changed, 33 insertions(+), 20 deletions(-)

More information about dataMeta at CRAN
Permanent link

Package strvalidator updated to version 2.0.0 with previous version 1.9.0 dated 2017-03-08

Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control. Tools to analyze data from internal validation of forensic short tandem repeat (STR) kits are provided. The tools are developed to provide the necessary data to conform with guidelines for internal validation issued by the European Network of Forensic Science Institutes (ENFSI) DNA Working Group, and the Scientific Working Group on DNA Analysis Methods (SWGDAM). A front-end graphical user interface is provided. More information about each function can be found in the respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskhan@ous-hf.no>

Diff between strvalidator versions 1.9.0 dated 2017-03-08 and 2.0.0 dated 2017-08-11

 DESCRIPTION                     |   14 
 MD5                             |  416 ++++++++++----------
 NAMESPACE                       |    7 
 NEWS                            |   32 +
 R/addColor.r                    |   19 
 R/addData.r                     |   14 
 R/addData_gui.r                 |   61 +--
 R/addDye_gui.r                  |   67 +--
 R/addMarker.r                   |   13 
 R/addMarker_gui.r               |   54 +-
 R/addOrder.r                    |   14 
 R/addSize.r                     |   14 
 R/addSize_gui.r                 |   53 +-
 R/auditTrail.R                  |only
 R/calculateAT.r                 |   73 ---
 R/calculateAT6.r                |    6 
 R/calculateAT6_gui.r            |   60 ++
 R/calculateAT_gui.r             |  117 ++---
 R/calculateAllele.r             |   16 
 R/calculateAllele_gui.r         |   37 +
 R/calculateCapillary.r          |    4 
 R/calculateCapillary_gui.r      |   43 +-
 R/calculateConcordance.r        |   26 -
 R/calculateConcordance_gui.r    |   60 +-
 R/calculateCopies.r             |   15 
 R/calculateCopies_gui.r         |   34 +
 R/calculateDropout.r            |   23 -
 R/calculateDropout_gui.r        |   64 +--
 R/calculateHb.r                 |   17 
 R/calculateHb_gui.r             |   59 +-
 R/calculateHeight.r             |   20 
 R/calculateHeight_gui.r         |   60 +-
 R/calculateLb.r                 |   36 -
 R/calculateLb_gui.r             |   64 +--
 R/calculateMixture.r            |    6 
 R/calculateMixture_gui.r        |   59 ++
 R/calculateOL.r                 |   17 
 R/calculateOL_gui.r             |   31 +
 R/calculateOverlap.r            |   15 
 R/calculateOverlap_gui.r        |   36 +
 R/calculatePeaks.r              |   15 
 R/calculatePeaks_gui.r          |   39 +
 R/calculatePullup.r             |   18 
 R/calculatePullup_gui.r         |   57 +-
 R/calculateRatio.r              |   18 
 R/calculateRatio_gui.r          |   65 +--
 R/calculateResultType.r         |   18 
 R/calculateResultType_gui.r     |   53 +-
 R/calculateSlope.r              |   20 
 R/calculateSlope_gui.r          |   54 +-
 R/calculateSpike.r              |   22 -
 R/calculateSpike_gui.r          |   45 +-
 R/calculateStutter.r            |   17 
 R/calculateStutter_gui.r        |   70 ++-
 R/checkSubset.r                 |    2 
 R/checkSubset_gui.r             |   29 -
 R/colConvert.r                  |    6 
 R/columns.r                     |   17 
 R/columns_gui.r                 |   63 +--
 R/combineBinsAndPanels.r        |    2 
 R/combine_gui.r                 |   42 +-
 R/cropData_gui.r                |   86 ++--
 R/editData_gui.r                |  119 +++--
 R/export.r                      |    5 
 R/export_gui.r                  |  197 +++++----
 R/filterProfile.r               |   25 -
 R/filterProfile_gui.r           |   68 +--
 R/generateEPG.r                 |    4 
 R/generateEPG_gui.r             |   45 +-
 R/getKit.r                      |    2 
 R/ggsave_gui.r                  |  130 +++---
 R/globals.R                     |    2 
 R/guessProfile.r                |   11 
 R/guessProfile_gui.r            |   40 +
 R/heightToPeak.r                |   19 
 R/import.r                      |   36 -
 R/import_gui.r                  |  242 +++++++-----
 R/listObjects.r                 |    2 
 R/makeKit_gui.r                 |   21 -
 R/maskAT.r                      |    6 
 R/modelDropout_gui.r            |  106 +++--
 R/plotAT_gui.r                  |   50 +-
 R/plotBalance_gui.r             |  101 ++---
 R/plotCapillary_gui.r           |   56 +-
 R/plotContamination_gui.r       |   40 +
 R/plotDistribution_gui.r        |   90 ++--
 R/plotDropout_gui.r             |   82 +---
 R/plotKit_gui.r                 |   33 -
 R/plotPeaks_gui.r               |   48 +-
 R/plotPrecision_gui.r           |   90 ++--
 R/plotPullup_gui.r              |   59 +-
 R/plotRatio_gui.r               |   44 +-
 R/plotResultType_gui.r          |   77 ++-
 R/plotSlope_gui.r               |   37 +
 R/plotStutter_gui.r             |   67 +--
 R/removeArtefact.r              |   16 
 R/removeArtefact_gui.r          |   36 +
 R/removeSpike.r                 |   10 
 R/removeSpike_gui.r             |   35 +
 R/saveObject.r                  |   10 
 R/scrambleAlleles.r             |    8 
 R/slim.r                        |   17 
 R/slim_gui.r                    |   59 +-
 R/sortMarker.r                  |    9 
 R/strvalidator-package.r        |   52 +-
 R/strvalidator.r                |  801 ++++++++++++++++++++--------------------
 R/tableBalance.r                |   12 
 R/tableBalance_gui.r            |   38 +
 R/tableCapillary.r              |    4 
 R/tableCapillary_gui.r          |   33 +
 R/tablePrecision.r              |    4 
 R/tablePrecision_gui.r          |   87 ++--
 R/tableStutter.r                |    8 
 R/tableStutter_gui.r            |   48 +-
 R/trim.r                        |   19 
 R/trim_gui.r                    |   70 +--
 README.md                       |   12 
 man/addColor.Rd                 |    4 
 man/addData_gui.Rd              |    2 
 man/addDye_gui.Rd               |    2 
 man/addMarker.Rd                |    2 
 man/addMarker_gui.Rd            |    2 
 man/addOrder.Rd                 |    2 
 man/addSize_gui.Rd              |    2 
 man/auditTrail.Rd               |only
 man/calculateAT.Rd              |    6 
 man/calculateAT6.Rd             |    2 
 man/calculateAT6_gui.Rd         |    2 
 man/calculateAT_gui.Rd          |    2 
 man/calculateAllele.Rd          |    4 
 man/calculateAllele_gui.Rd      |    2 
 man/calculateCapillary_gui.Rd   |    2 
 man/calculateConcordance_gui.Rd |    2 
 man/calculateCopies.Rd          |    2 
 man/calculateCopies_gui.Rd      |    2 
 man/calculateDropout.Rd         |    4 
 man/calculateDropout_gui.Rd     |    2 
 man/calculateHb.Rd              |    2 
 man/calculateHb_gui.Rd          |    2 
 man/calculateHeight_gui.Rd      |    2 
 man/calculateLb.Rd              |    6 
 man/calculateLb_gui.Rd          |    2 
 man/calculateMixture.Rd         |    2 
 man/calculateMixture_gui.Rd     |    2 
 man/calculateOL.Rd              |    6 
 man/calculateOL_gui.Rd          |    4 
 man/calculateOverlap.Rd         |    6 
 man/calculateOverlap_gui.Rd     |    6 
 man/calculatePeaks.Rd           |    2 
 man/calculatePeaks_gui.Rd       |    2 
 man/calculatePullup_gui.Rd      |    2 
 man/calculateRatio_gui.Rd       |    2 
 man/calculateResultType.Rd      |    2 
 man/calculateResultType_gui.Rd  |    2 
 man/calculateSlope.Rd           |    4 
 man/calculateSlope_gui.Rd       |    2 
 man/calculateSpike.Rd           |    6 
 man/calculateSpike_gui.Rd       |    2 
 man/calculateStutter.Rd         |    2 
 man/calculateStutter_gui.Rd     |    2 
 man/checkSubset.Rd              |    2 
 man/checkSubset_gui.Rd          |    2 
 man/columns_gui.Rd              |    2 
 man/combineBinsAndPanels.Rd     |    2 
 man/combine_gui.Rd              |    2 
 man/cropData_gui.Rd             |    6 
 man/editData_gui.Rd             |   13 
 man/export.Rd                   |    1 
 man/export_gui.Rd               |   10 
 man/filterProfile.Rd            |    4 
 man/filterProfile_gui.Rd        |    2 
 man/generateEPG.Rd              |    4 
 man/generateEPG_gui.Rd          |    2 
 man/getKit.Rd                   |    2 
 man/guessProfile.Rd             |    2 
 man/guessProfile_gui.Rd         |    2 
 man/heightToPeak.Rd             |    9 
 man/import.Rd                   |    3 
 man/listObjects.Rd              |    2 
 man/makeKit_gui.Rd              |    2 
 man/modelDropout_gui.Rd         |   14 
 man/plotAT_gui.Rd               |    4 
 man/plotBalance_gui.Rd          |    6 
 man/plotCapillary_gui.Rd        |    6 
 man/plotContamination_gui.Rd    |    4 
 man/plotDistribution_gui.Rd     |    4 
 man/plotDropout_gui.Rd          |    4 
 man/plotKit_gui.Rd              |    2 
 man/plotPeaks_gui.Rd            |    8 
 man/plotPrecision_gui.Rd        |    4 
 man/plotPullup_gui.Rd           |    6 
 man/plotRatio_gui.Rd            |    4 
 man/plotResultType_gui.Rd       |    8 
 man/plotSlope_gui.Rd            |    4 
 man/plotStutter_gui.Rd          |    4 
 man/ref1.Rd                     |    2 
 man/ref11.Rd                    |    2 
 man/ref4.Rd                     |    4 
 man/removeArtefact_gui.Rd       |    2 
 man/removeSpike_gui.Rd          |    2 
 man/saveObject.Rd               |    2 
 man/scrambleAlleles.Rd          |    4 
 man/slim.Rd                     |    4 
 man/slim_gui.Rd                 |    2 
 man/strvalidator-package.Rd     |   44 +-
 man/tableBalance_gui.Rd         |    2 
 man/tableCapillary_gui.Rd       |    2 
 man/tablePrecision_gui.Rd       |    2 
 man/tableStutter_gui.Rd         |    2 
 man/trim_gui.Rd                 |    2 
 210 files changed, 3433 insertions(+), 2795 deletions(-)

More information about strvalidator at CRAN
Permanent link

Package meta updated to version 4.8-4 with previous version 4.8-3 dated 2017-07-22

Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from 'RevMan 5'; - prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression (if R package 'metafor' is installed); - generalised linear mixed models (if R packages 'metafor', 'lme4', 'numDeriv', and 'BiasedUrn' are installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>

Diff between meta versions 4.8-3 dated 2017-07-22 and 4.8-4 dated 2017-08-11

 DESCRIPTION            |    8 -
 MD5                    |   57 ++++++------
 NAMESPACE              |    3 
 NEWS                   |   44 +++++++++
 R/bubble.metareg.R     |   13 ++
 R/chkmiss.R            |    2 
 R/chknumeric.R         |    2 
 R/forest-internal.R    |   26 ++---
 R/forest.meta.R        |   26 ++---
 R/is.cor.R             |only
 R/is.prop.R            |only
 R/is.rate.R            |only
 R/meta-internal.R      |    3 
 R/metabias.default.R   |  158 +++++----------------------------
 R/metacor.R            |    2 
 R/metacum.R            |    4 
 R/metagen.R            |    4 
 R/metainf.R            |    4 
 R/metaprop.R           |    4 
 R/metarate.R           |    2 
 R/print.meta.R         |   12 +-
 R/print.summary.meta.R |   29 +++++-
 R/radial.default.R     |   74 ++++++---------
 R/setchar.R            |    2 
 R/settings.meta.R      |   11 +-
 R/summary.meta.R       |   38 +++++---
 R/trimfill.default.R   |  232 +++++--------------------------------------------
 R/trimfill.meta.R      |  118 +++++++++++++++++++++---
 R/xlab.R               |    4 
 man/forest.Rd          |    6 +
 man/labbe.Rd           |   11 +-
 31 files changed, 398 insertions(+), 501 deletions(-)

More information about meta at CRAN
Permanent link

New package HEMDAG with initial version 1.0.0
Package: HEMDAG
Title: Hierarchical Ensemble Methods for Directed Acyclic Graphs
Version: 1.0.0
Author: Marco Notaro [aut, cre] and Giorgio Valentini [aut] (AnacletoLab, Dipartimento di Informatica, Universita' degli Studi di Milano)
Maintainer: Marco Notaro <marco.notaro@unimi.it>
Description: An implementation of Hierarchical Ensemble Methods for DAGs: 'HTD-DAG' (Hierarchical Top Down) and 'TPR-DAG' (True Path Rule). 'HEMDAG' can be used to enhance the predictions of virtually any flat learning method, by taking into account the hierarchical nature of the classes of a bio-ontology. 'HEMDAG' is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but it can be also safely applied to tree-structured taxonomies (as FunCat), since trees are DAGs. 'HEMDAG' scale nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini, Prediction of Human Phenotype Ontology terms by means of Hierarchical Ensemble methods, BMC Bioinformatics 2017).
Depends: R (>= 3.4.1)
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Repository: CRAN
NeedsCompilation: no
Imports: graph, RBGL, PerfMeas, precrec, preprocessCore, methods
Suggests: Rgraphviz
RoxygenNote: 6.0.1
Packaged: 2017-08-11 19:25:58 UTC; marco
Date/Publication: 2017-08-11 21:56:15 UTC

More information about HEMDAG at CRAN
Permanent link

Package rtimes updated to version 0.5.0 with previous version 0.4.0 dated 2017-05-10

Title: Client for New York Times 'APIs'
Description: Interface to Congress, Campaign Finance, Article Search, and Geographic 'APIs' from the New York Times (<http://developer.nytimes.com/>) and 'ProPublica' (<https://www.propublica.org/datastore/apis>). This client covers a subset of the New York Times and 'ProPublica' 'APIs'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rtimes versions 0.4.0 dated 2017-05-10 and 0.5.0 dated 2017-08-11

 DESCRIPTION                     |   14 +--
 MD5                             |   98 +++++++++++------------
 NAMESPACE                       |    4 
 NEWS.md                         |   22 ++++-
 R/as_search.R                   |   12 +-
 R/cf_candidate_details.R        |    6 -
 R/cf_candidate_leaders.R        |    5 -
 R/cf_candidate_new.R            |    5 -
 R/cf_candidate_search.R         |   12 +-
 R/cf_candidate_state.R          |    5 -
 R/cg_billscosponsor.R           |    8 +
 R/cg_memberappear.R             |    5 -
 R/cg_memberbioroles.R           |    6 +
 R/cg_memberbystatedistrict.R    |    6 +
 R/cg_memberlist.R               |    6 +
 R/cg_membersleaving.R           |    6 +
 R/cg_membersponsorcompare.R     |    8 +
 R/cg_membervotecompare.R        |    8 +
 R/cg_membervotepositions.R      |    6 +
 R/cg_newmembers.R               |    6 +
 R/cg_rollcallvote.R             |   14 ++-
 R/geo_search.R                  |   12 +-
 R/rtimes-package.R              |   68 +++++++++-------
 R/zzz.R                         |   17 ++--
 README.md                       |   62 +++++---------
 build/vignette.rds              |binary
 inst/doc/rtimes_vignette.Rmd    |  170 +++++++++++++++++-----------------------
 inst/doc/rtimes_vignette.html   |  168 ++++++++++++++++-----------------------
 man/as_search.Rd                |    6 +
 man/cf_candidate_details.Rd     |    9 +-
 man/cf_candidate_leaders.Rd     |   27 ++++--
 man/cf_candidate_new.Rd         |    9 +-
 man/cf_candidate_search.Rd      |   13 ++-
 man/cf_candidate_state.Rd       |   13 ++-
 man/cg_billscosponsor.Rd        |   24 ++++-
 man/cg_memberappear.Rd          |   26 +++++-
 man/cg_memberbioroles.Rd        |   24 ++++-
 man/cg_memberbystatedistrict.Rd |   24 ++++-
 man/cg_membersleaving.Rd        |   24 ++++-
 man/cg_memberslist.Rd           |   24 ++++-
 man/cg_membersponsorcompare.Rd  |   26 +++++-
 man/cg_membervotecompare.Rd     |   24 ++++-
 man/cg_membervotepositions.Rd   |   24 ++++-
 man/cg_newmembers.Rd            |   24 ++++-
 man/cg_rollcallvote.Rd          |   26 +++++-
 man/geo_search.Rd               |    7 -
 man/rtimes-package.Rd           |   73 ++++++++++-------
 tests/testthat/test-as_search.R |    2 
 tools/unnamed-chunk-9-1.png     |binary
 vignettes/rtimes_vignette.Rmd   |  170 +++++++++++++++++-----------------------
 50 files changed, 795 insertions(+), 563 deletions(-)

More information about rtimes at CRAN
Permanent link

Package TreatmentSelection updated to version 2.1.1 with previous version 2.1.0 dated 2017-07-25

Title: Evaluate Treatment Selection Biomarkers
Description: A suite of descriptive and inferential methods designed to evaluate one or more biomarkers for their ability to guide patient treatment recommendations. Package includes functions to assess the calibration of risk models; and plot, evaluate, and compare markers. Please see the reference Janes H, Brown MD, Huang Y, et al. (2014) <doi:10.1515/ijb-2012-0052> for further details.
Author: Marshall Brown and Holly Janes
Maintainer: Marshall Brown <mdbrown@fhcrc.org>

Diff between TreatmentSelection versions 2.1.0 dated 2017-07-25 and 2.1.1 dated 2017-08-11

 DESCRIPTION                |   14 +++++++-------
 MD5                        |   11 ++++++-----
 NEWS                       |    5 +++++
 R/trtsel.R                 |    2 +-
 inst/example/tutorial.Rmd  |    4 +++-
 inst/example/tutorial.html |only
 man/trtsel.Rd              |    2 +-
 7 files changed, 23 insertions(+), 15 deletions(-)

More information about TreatmentSelection at CRAN
Permanent link

New package IAbin with initial version 1.0
Package: IAbin
Type: Package
Title: Plotting N-T Plane for Decision on Performing an Interim Analysis
Version: 1.0
Date: 2017-08-11
Author: Kyongsun Pak
Maintainer: Kyongsun Pak <pakk@pharm.kitasato-u.ac.jp>
Description: In randomized-controlled trials, interim analyses are often planned for possible early trial termination to claim superiority or futility of a new therapy. Blinded data also have information about the potential treatment difference between the groups. We developed a blinded data monitoring tool that enables investigators to predict whether they observe such an unblinded interim analysis results that supports early termination of the trial. Investigators may skip some of the planned interim analyses if an early termination is unlikely. This tool will provide reference information about N: Sample size at interim analysis, and T: Total number of responders at interim analysis for decision on performing an interim analysis.
License: GPL (>= 2)
VignetteBuilder: knitr
RoxygenNote: 6.0.1
Suggests: testthat, evaluate, knitr
Imports: graphics, stats
NeedsCompilation: no
Packaged: 2017-08-11 18:17:36 UTC; pakk
Repository: CRAN
Date/Publication: 2017-08-11 18:52:55 UTC

More information about IAbin at CRAN
Permanent link

New package vanddraabe with initial version 1.0.0
Package: vanddraabe
Type: Package
Title: Identification and Statistical Analysis of Conserved Waters in Proteins
Description: Identify and analyze conserved waters within crystallographic protein structures and molecular dynamics simulation trajectories. Statistical parameters for each water cluster, informative graphs, and a PyMOL session file to visually explore the conserved waters and protein are returned. Hydrophilicity is the propensity of waters to congregate near specific protein atoms and is related to conserved waters. An informatics derived set of hydrophilicity values are provided based on a large, high-quality X-ray protein structure dataset.
Version: 1.0.0
Date: 2017-08-10
Depends: R (>= 3.3.3)
Imports: bio3d (>= 2.3-1), cowplot (>= 0.7.0), fastcluster (>= 1.1.22), ggplot2 (>= 2.2.1), openxlsx (>= 4.0.17), reshape2 (>= 1.4.2), scales (>= 0.4.1)
Suggests: knitr, rmarkdown, testthat
Authors@R: person("Emilio Xavier", "Esposito", email = "emilio@exeResearch.com", role = c("aut", "cre"))
URL: http://www.exeResearch.com/vanddraabe.html, https://github.com/exeResearch/vanddraabe/
BugReports: https://github.com/exeResearch/vanddraabe/issues
License: MIT + file LICENSE
LazyData: TRUE
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2017-08-10 20:34:49 UTC; emilio
Author: Emilio Xavier Esposito [aut, cre]
Maintainer: Emilio Xavier Esposito <emilio@exeResearch.com>
Repository: CRAN
Date/Publication: 2017-08-11 16:14:58 UTC

More information about vanddraabe at CRAN
Permanent link

Package OpenML updated to version 1.5 with previous version 1.4 dated 2017-06-22

Title: Exploring Machine Learning Better, Together
Description: 'OpenML.org' is an online machine learning platform where researchers can easily download and upload data sets, share machine learning tasks and experiments and organize them online to work and collaborate more effectively. We provide an R interface to the OpenML REST API in order to download and upload data sets, tasks, flows and runs, see <http://www.openml.org/guide> for more information.
Author: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>, Bernd Bischl <bernd_bischl@gmx.net>, Dominik Kirchhoff <dom.kirchhoff@gmail.com>, Michel Lang <michellang@gmail.com>, Benjamin Hofner <benjamin.hofner@fau.de>, Jakob Bossek <j.bossek@gmail.com>, Pascal Kerschke <kerschke@uni-muenster.de>, Joaquin Vanschoren <joaquin.vanschoren@gmail.com>
Maintainer: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>

Diff between OpenML versions 1.4 dated 2017-06-22 and 1.5 dated 2017-08-11

 DESCRIPTION                        |    6 ++--
 MD5                                |   45 ++++++++++++++++++++-----------------
 NAMESPACE                          |    3 ++
 NEWS                               |    5 ++++
 R/config_helpers.R                 |    8 +++---
 R/download.R                       |   26 ++++++++++++---------
 R/getOMLStudy.R                    |only
 R/listOMLStudies.R                 |only
 R/loadOMLConfig.R                  |    5 ++--
 R/zzz.R                            |    2 -
 man/getOMLDataSet.Rd               |    2 -
 man/getOMLDataSetQualities.Rd      |    2 -
 man/getOMLFlow.Rd                  |    2 -
 man/getOMLRun.Rd                   |    2 -
 man/getOMLStudy.Rd                 |only
 man/getOMLTask.Rd                  |    2 -
 man/listOMLDataSetQualities.Rd     |    1 
 man/listOMLDataSets.Rd             |    1 
 man/listOMLEstimationProcedures.Rd |    1 
 man/listOMLEvaluationMeasures.Rd   |    1 
 man/listOMLFlows.Rd                |    2 -
 man/listOMLRuns.Rd                 |    2 -
 man/listOMLStudies.Rd              |only
 man/listOMLTaskTypes.Rd            |    2 -
 man/listOMLTasks.Rd                |    1 
 vignettes/openml-cheatsheet.pdf    |only
 26 files changed, 72 insertions(+), 49 deletions(-)

More information about OpenML at CRAN
Permanent link

Package ecoseries updated to version 0.1.4 with previous version 0.1.3 dated 2017-05-04

Title: An R Interface to Brazilian Central Bank and Sidra APIs and the IPEA Data
Description: Creates an R interface to the Bacen <http://api.bcb.gov.br/> and Sidra <http://api.sidra.ibge.gov.br> APIs and IPEA data <http://www.ipeadata.gov.br/Default.aspx>.
Author: Fernando Teixeira [aut, cre], Jonatha Azevedo [aut]
Maintainer: Fernando Teixeira <fernando.teixeira@fgv.br>

Diff between ecoseries versions 0.1.3 dated 2017-05-04 and 0.1.4 dated 2017-08-11

 DESCRIPTION            |   10 +--
 MD5                    |   14 ++---
 NAMESPACE              |    1 
 R/aux_ipeadata.R       |   32 +++++++-----
 R/series_ipeadata.R    |    2 
 R/series_sidra.R       |  128 +++++++++++++++++++++++++++----------------------
 man/series_ipeadata.Rd |    2 
 man/series_sidra.Rd    |   17 ++----
 8 files changed, 113 insertions(+), 93 deletions(-)

More information about ecoseries at CRAN
Permanent link

Package RIA updated to version 1.2.0 with previous version 1.1.0 dated 2017-06-08

Title: Radiomics Image Analysis Toolbox for Grayscale Images
Description: Radiomics image analysis toolbox for grayscale 2D and 3D images. RIA calculates first-order, gray level co-occurrence matrix, gray level run length matrix and geometry-based statistics. Almost all calculations are done using vectorized formulas to optimize run speeds. Calculation of several thousands of parameters only takes minutes on a single core of a conventional PC.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <marton.kolossvary@cirg.hu>

Diff between RIA versions 1.1.0 dated 2017-06-08 and 1.2.0 dated 2017-08-11

 RIA-1.1.0/RIA/R/dichotomize.R    |only
 RIA-1.1.0/RIA/man/dichotomize.Rd |only
 RIA-1.2.0/RIA/DESCRIPTION        |    8 
 RIA-1.2.0/RIA/MD5                |   50 +-
 RIA-1.2.0/RIA/NAMESPACE          |    4 
 RIA-1.2.0/RIA/R/check_data_in.R  |    4 
 RIA-1.2.0/RIA/R/discretize.R     |only
 RIA-1.2.0/RIA/R/first_order.R    |   18 
 RIA-1.2.0/RIA/R/geometry.R       |   26 -
 RIA-1.2.0/RIA/R/glcm.R           |   24 -
 RIA-1.2.0/RIA/R/glcm_all.R       |only
 RIA-1.2.0/RIA/R/glcm_stat.R      |   10 
 RIA-1.2.0/RIA/R/glrlm.R          |  297 ++++++++-------
 RIA-1.2.0/RIA/R/glrlm_all.R      |only
 RIA-1.2.0/RIA/R/glrlm_stat.R     |   10 
 RIA-1.2.0/RIA/R/load_dicom.R     |    4 
 RIA-1.2.0/RIA/inst/doc/RIA.R     |   56 +-
 RIA-1.2.0/RIA/inst/doc/RIA.Rmd   |  730 +++++++++++++++++++--------------------
 RIA-1.2.0/RIA/inst/doc/RIA.html  |  522 +++++++++++++++++++++++----
 RIA-1.2.0/RIA/man/discretize.Rd  |only
 RIA-1.2.0/RIA/man/first_order.Rd |   14 
 RIA-1.2.0/RIA/man/geometry.Rd    |   22 -
 RIA-1.2.0/RIA/man/glcm.Rd        |   18 
 RIA-1.2.0/RIA/man/glcm_all.Rd    |only
 RIA-1.2.0/RIA/man/glcm_stat.Rd   |    8 
 RIA-1.2.0/RIA/man/glrlm.Rd       |   37 +
 RIA-1.2.0/RIA/man/glrlm_all.Rd   |only
 RIA-1.2.0/RIA/man/glrlm_stat.Rd  |    8 
 RIA-1.2.0/RIA/man/load_dicom.Rd  |    4 
 RIA-1.2.0/RIA/vignettes/RIA.Rmd  |  730 +++++++++++++++++++--------------------
 30 files changed, 1533 insertions(+), 1071 deletions(-)

More information about RIA at CRAN
Permanent link

New package kaphom with initial version 0.1.0
Package: kaphom
Type: Package
Title: Test the Homogeneity of Kappa Statistics
Version: 0.1.0
Author: Muammer Albayrak
Maintainer: Muammer Albayrak <m.albayrak@ktu.edu.tr>
Description: Tests the homogeneity of intraclass kappa statistics obtained from independent studies or a stratified study with binary results. It is desired to compare the kappa statistics obtained in multi-center studies or in a single stratified study to give a common or summary kappa using all available information. If the homogeneity test of these kappa statistics is not rejected, then it is possible to make inferences over a single kappa statistic that summarizes all the studies. Jun-mo Nam (2003) <doi:10.1111/j.0006-341X.2003.00118.x> Jun-mo Nam (2005) <doi:10.1002/sim.2321>Mousumi Banerjee, Michelle Capozzoli, Laura McSweeney,Debajyoti Sinha (1999) <doi:10.2307/3315487> Allan Donner, Michael Eliasziw, Neil Klar (1996) <doi:10.2307/2533154>.
Imports: stats
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-08-11 13:01:10 UTC; Muammer
Repository: CRAN
Date/Publication: 2017-08-11 13:28:31 UTC

More information about kaphom at CRAN
Permanent link

New package survivALL with initial version 0.9.0
Package: survivALL
Title: Continuous Biomarker Assessment by Exhaustive Survival Analysis
Version: 0.9.0
Authors@R: person("Dominic", "Pearce", email = "dominic.pearce@ed.ac.uk", role = c("aut", "cre"))
Description: In routine practice, biomarker performance is calculated by splitting a patient cohort at some arbitrary level, often by median gene expression. The logic behind this is to divide patients into “high” or “low” expression groups that in turn correlate with either good or poor prognosis. However, this median-split approach assumes that the data set composition adheres to a strict 1:1 proportion of high vs. low expression, that for every one “low” there is an equivalent “high”. In reality, data sets are often heterogeneous in their composition (Perou, CM et al., 2000 <doi:10.1038/35021093>)- i.e. this 1:1 relationship is unlikely to exist and the true relationship unknown. Given this limitation, it remains difficult to determine where the most significant separation should be made. For example, estrogen receptor (ER) status determined by immunohistochemistry is standard practice in predicting hormone therapy response, where ER is found in an ~1:3 ratio (-:+) in the populationi (Selli, C et al., 2016 <doi:10.1186/s13058-016-0779-0>). We would expect therefore, upon dividing patients by ER expression, 25% to be classified “low” and 75% “high”, and an otherwise 50-50 split to incorrectly classify 25% of our patient cohort, rendering our survival estimate under powered. 'survivALL' is a data-driven approach to calculate the relative survival estimates for all possible points of separation - i.e. at all possible ratios of “high” vs. “low” - allowing a measure’s relationship with survival to be more reliably determined and quantified. We see this as a solution to a flaw in common research practice, namely the failure of a true biomarker as part of a meta-analysis.
Depends: R (>= 3.3.1)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
biocViews:
Imports: survival, survcomp, survsim, Biobase, desiR, readr, broom, magrittr, ggplot2, cowplot, ggthemes, viridis, data.table, pander, png, testthat
Suggests: GGally, knitr, rmarkdown
RoxygenNote: 6.0.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-08-11 12:08:10 UTC; dom
Author: Dominic Pearce [aut, cre]
Maintainer: Dominic Pearce <dominic.pearce@ed.ac.uk>
Repository: CRAN
Date/Publication: 2017-08-11 12:35:25 UTC

More information about survivALL at CRAN
Permanent link

Package depend.truncation updated to version 2.8 with previous version 2.7 dated 2017-07-30

Title: Statistical Inference for Parametric and Semiparametric Models Based on Dependently Truncated Data
Description: Suppose that one can observe bivariate random variables (X, Y) only when X<=Y holds. Data (Xj, Yj), subject to Xj<=Yj, for all j=1,...,n, are called truncated data. For truncated data, several different approaches are implemented for statistical inference on (X, Y), when X and Y are dependent. Also included is truncated data on the number of deaths at each year (1963-1980) for Japanese male centenarians.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

Diff between depend.truncation versions 2.7 dated 2017-07-30 and 2.8 dated 2017-08-11

 DESCRIPTION                      |    8 ++++----
 MD5                              |    6 +++---
 R/PMLE.Clayton.Exponential.R     |    9 ++++-----
 man/depend.truncation-package.Rd |    2 +-
 4 files changed, 12 insertions(+), 13 deletions(-)

More information about depend.truncation at CRAN
Permanent link

New package rasterList with initial version 0.5.8
Package: rasterList
Maintainer: Emanuele Cordano <emanuele.cordano@ext.ec.europa.eu>
License: GPL (>= 3)
Title: A Raster Where Cells are Generic Objects
Type: Package
Author: Emanuele Cordano, Unit D.02 Water and Marine Resources,Joint Research Centre of the European Commission
Description: A S4 class has been created such that complex operations can be executed on each cells of a raster map. The raster of objects contains the traditional raster map with the addition of a list of generic objects: one object for each raster cells. It allows to write few lines of R code for complex map algebra. Two environmental applications about frequency analysis of raster map of precipitation and creation of a raster map of soil water retention curves have been presented.
Version: 0.5.8
Date: 2017-08-11
Repository: CRAN
Depends: R(>= 3.0.1),raster,methods
Suggests: lmom,testthat,sp,soilwater
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-08-10 22:00:25 UTC; ecor
Date/Publication: 2017-08-11 09:42:42 UTC

More information about rasterList at CRAN
Permanent link

Package biospear updated to version 1.0.1 with previous version 1.0.0 dated 2017-05-13

Title: Biomarker Selection in Penalized Regression Models
Description: Provides some tools for developing and validating prediction models, estimate expected survival of patients and visualize them graphically. Most of the implemented methods are based on penalized regressions such as: the lasso (Tibshirani R (1996)), the elastic net (Zou H et al. (2005) <doi:10.1111/j.1467-9868.2005.00503.x>), the adaptive lasso (Zou H (2006) <doi:10.1198/016214506000000735>), the stability selection (Meinshausen N et al. (2010) <doi:10.1111/j.1467-9868.2010.00740.x>), some extensions of the lasso (Ternes et al. (2016) <doi:10.1002/sim.6927>), some methods for the interaction setting (Ternes N et al. (2016) <doi:10.1002/bimj.201500234>), or others. A function generating simulated survival data set is also provided.
Author: Nils Ternes [aut, cre], Federico Rotolo [aut], Stefan Michiels [ctr]
Maintainer: Nils Ternes <nils.ternes@yahoo.com>

Diff between biospear versions 1.0.0 dated 2017-05-13 and 1.0.1 dated 2017-08-11

 DESCRIPTION    |   10 ++----
 MD5            |   16 +++++-----
 R/BMsel.R      |   12 +++++++
 R/expSurv.R    |   41 +++++++++++++-------------
 R/gboost.R     |    1 
 R/predRes.R    |   88 ++++++++++++++++++++++++++++-----------------------------
 man/BMsel.Rd   |    6 +++
 man/expSurv.Rd |   12 +++----
 man/predRes.Rd |   18 +++++------
 9 files changed, 110 insertions(+), 94 deletions(-)

More information about biospear at CRAN
Permanent link

Package rcv updated to version 0.2.1 with previous version 0.2.0 dated 2017-06-14

Title: Ranked Choice Voting
Description: A collection of ranked choice voting data and functions to manipulate, run elections with, and visualize this data and others. It can bring in raw data, transform it into a ballot you can read, and return election results for an RCV contest.
Author: Jay Lee [aut], Matthew Yancheff [aut, cre], Reed College [cph]
Maintainer: Matthew Yancheff <yanchefm@reed.edu>

Diff between rcv versions 0.2.0 dated 2017-06-14 and 0.2.1 dated 2017-08-11

 DESCRIPTION            |    8 ++++----
 MD5                    |   10 +++++-----
 NEWS.md                |    4 ++--
 R/cleaning_functions.R |    2 +-
 R/plot_functions.R     |    4 ++--
 README.md              |   40 +++++++++++++++++++++++++---------------
 6 files changed, 39 insertions(+), 29 deletions(-)

More information about rcv at CRAN
Permanent link

Package valaddin updated to version 0.1.2 with previous version 0.1.0 dated 2017-03-24

Title: Functional Input Validation
Description: A set of basic tools to transform functions into functions with input validation checks, in a manner suitable for both programmatic and interactive use.
Author: Eugene Ha [aut, cre]
Maintainer: Eugene Ha <eha@posteo.de>

Diff between valaddin versions 0.1.0 dated 2017-03-24 and 0.1.2 dated 2017-08-11

 DESCRIPTION                      |   11 
 MD5                              |   64 +-
 NAMESPACE                        |    6 
 NEWS.md                          |   92 +++
 R/call.R                         |   17 
 R/checkers.R                     |   63 +-
 R/checklist.R                    |    8 
 R/components.R                   |   30 -
 R/firmly.R                       |  291 +++++++----
 R/rawrd.R                        |   54 +-
 R/scope.R                        |   76 +--
 R/utils.R                        |   13 
 R/validate.R                     |only
 README.md                        |  226 ++++-----
 build/vignette.rds               |binary
 inst/doc/valaddin.R              |    2 
 inst/doc/valaddin.Rmd            |   19 
 inst/doc/valaddin.html           |  962 +++++++++++++++++++++++++--------------
 man/bare-type-checkers.Rd        |    5 
 man/components.Rd                |   21 
 man/firmly.Rd                    |   71 ++
 man/misc-checkers.Rd             |   11 
 man/scalar-type-checkers.Rd      |    5 
 man/type-checkers.Rd             |   19 
 man/validate.Rd                  |only
 tests/testthat/helper.R          |    2 
 tests/testthat/test-checkers.R   |   43 +
 tests/testthat/test-components.R |   45 +
 tests/testthat/test-firmly.R     |   83 ++-
 tests/testthat/test-loosely.R    |  103 ----
 tests/testthat/test-print.R      |   48 +
 tests/testthat/test-scope.R      |    2 
 tests/testthat/test-validation.R |  211 +++++++-
 vignettes/valaddin.Rmd           |   19 
 34 files changed, 1727 insertions(+), 895 deletions(-)

More information about valaddin at CRAN
Permanent link

Package smotefamily updated to version 1.1 with previous version 1.0 dated 2016-09-08

Title: A Collection of Oversampling Techniques for Class Imbalance Problem Based on SMOTE
Description: A collection of various oversampling techniques developed from SMOTE is provided. SMOTE is a oversampling technique which synthesizes a new minority instance between a pair of one minority instance and one of its K nearest neighbor. (see <https://www.jair.org/media/953/live-953-2037-jair.pdf> for more information) Other techniques adopt this concept with other criteria in order to generate balanced dataset for class imbalance problem.
Author: Wacharasak Siriseriwan [aut, cre]
Maintainer: Wacharasak Siriseriwan <wacharasak.s@gmail.com>

Diff between smotefamily versions 1.0 dated 2016-09-08 and 1.1 dated 2017-08-11

 DESCRIPTION |    8 ++++----
 MD5         |    6 +++---
 R/DBSMOTE.R |    3 ++-
 R/SMOTE.R   |    2 +-
 4 files changed, 10 insertions(+), 9 deletions(-)

More information about smotefamily at CRAN
Permanent link

Package rjmcmc updated to version 0.3.2 with previous version 0.3.01 dated 2017-08-03

Title: Reversible-Jump MCMC Using Post-Processing
Description: Performs reversible-jump Markov chain Monte Carlo (Green, 1995) <doi:10.2307/2337340>, specifically the restriction introduced by Barker & Link (2013) <doi:10.1080/00031305.2013.791644>. By utilising a 'universal parameter' space, RJMCMC is treated as a Gibbs sampling problem. Previously-calculated posterior distributions are used to quickly estimate posterior model probabilities. Jacobian matrices are found using automatic differentiation.
Author: Nick Gelling [aut, cre], Matthew R. Schofield [aut], Richard J. Barker [aut]
Maintainer: Nick Gelling <ngelling@maths.otago.ac.nz>

Diff between rjmcmc versions 0.3.01 dated 2017-08-03 and 0.3.2 dated 2017-08-11

 rjmcmc-0.3.01/rjmcmc/vignettes/framed.sty  |only
 rjmcmc-0.3.2/rjmcmc/DESCRIPTION            |    6 +++---
 rjmcmc-0.3.2/rjmcmc/MD5                    |    5 ++---
 rjmcmc-0.3.2/rjmcmc/inst/doc/rjmcmcVig.pdf |binary
 4 files changed, 5 insertions(+), 6 deletions(-)

More information about rjmcmc at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.