Mon, 07 Jul 2014

Package icd9 updated to version 0.3 with previous version 0.2.1 dated 2014-07-02

Title: tools for working with ICD-9 codes, and finding comorbidities
Description: This package allows accurate manipulation, validation and comparison of ICD-9-CM (clinical modification) codes. Although ICD-9 codes appear numeric, this is not the case, since trailing zeroes, and a mixture of decimal and non-decimal "short" format codes exist. Tools to map ICD-9 codes to co-morbidities are also provided, with mappings from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included.
Author: Jack O. Wasey [aut, cre]
Maintainer: Jack O. Wasey

Diff between icd9 versions 0.2.1 dated 2014-07-02 and 0.3 dated 2014-07-07

 icd9-0.2.1/icd9/R/icd9.R                           |only
 icd9-0.2.1/icd9/man/getInvalidDecimalIcd9.Rd       |only
 icd9-0.2.1/icd9/man/grapes-i9mj-grapes.Rd          |only
 icd9-0.2.1/icd9/man/icd9AddLeadingZeroesDecimal.Rd |only
 icd9-0.2.1/icd9/man/icd9AddLeadingZeroesMajor.Rd   |only
 icd9-0.2.1/icd9/man/icd9AddLeadingZeroesShort.Rd   |only
 icd9-0.2.1/icd9/man/icd9DropZeroFromDecimal.Rd     |only
 icd9-0.3/icd9/DESCRIPTION                          |   10 
 icd9-0.3/icd9/MD5                                  |  133 ++++----
 icd9-0.3/icd9/NAMESPACE                            |   10 
 icd9-0.3/icd9/NEWS                                 |   17 +
 icd9-0.3/icd9/R/comorbid.R                         |  100 ++----
 icd9-0.3/icd9/R/convert.R                          |only
 icd9-0.3/icd9/R/datadocs.R                         |   53 +++
 icd9-0.3/icd9/R/explain.R                          |only
 icd9-0.3/icd9/R/manip.R                            |only
 icd9-0.3/icd9/R/parse.R                            |   44 ++
 icd9-0.3/icd9/R/ranges.R                           |only
 icd9-0.3/icd9/R/util.R                             |   90 ++++-
 icd9-0.3/icd9/R/valid.R                            |  144 ++++++--
 icd9-0.3/icd9/README.md                            |   30 -
 icd9-0.3/icd9/data/ahrqComorbid.RData              |binary
 icd9-0.3/icd9/data/ahrqComorbidAll.RData           |binary
 icd9-0.3/icd9/data/elixhauserComorbid.RData        |binary
 icd9-0.3/icd9/data/icd9CmChapters.rda              |only
 icd9-0.3/icd9/inst/doc/icd9.R                      |   57 ++-
 icd9-0.3/icd9/inst/doc/icd9.Rnw                    |  101 ++++--
 icd9-0.3/icd9/inst/doc/icd9.pdf                    |binary
 icd9-0.3/icd9/man/allIsNumeric.Rd                  |    7 
 icd9-0.3/icd9/man/asCharacterNoWarn.Rd             |    3 
 icd9-0.3/icd9/man/asNumericNoWarn.Rd               |    5 
 icd9-0.3/icd9/man/icd9AddLeadingZeroes.Rd          |only
 icd9-0.3/icd9/man/icd9ChapterShort.Rd              |only
 icd9-0.3/icd9/man/icd9ChildrenDecimal.Rd           |    7 
 icd9-0.3/icd9/man/icd9ChildrenShort.Rd             |   17 -
 icd9-0.3/icd9/man/icd9CmChapters.Rd                |only
 icd9-0.3/icd9/man/icd9CmDesc.Rd                    |   30 +
 icd9-0.3/icd9/man/icd9Comorbidities.Rd             |    5 
 icd9-0.3/icd9/man/icd9CondenseShort.Rd             |    4 
 icd9-0.3/icd9/man/icd9CondenseToExplainShort.Rd    |    4 
 icd9-0.3/icd9/man/icd9DecimalToMajor.Rd            |only
 icd9-0.3/icd9/man/icd9DecimalToParts.Rd            |    9 
 icd9-0.3/icd9/man/icd9DecimalToShort.Rd            |   21 -
 icd9-0.3/icd9/man/icd9DropLeadingZeroes.Rd         |only
 icd9-0.3/icd9/man/icd9ExpandMinor.Rd               |    7 
 icd9-0.3/icd9/man/icd9ExpandRangeDecimal.Rd        |    3 
 icd9-0.3/icd9/man/icd9ExpandRangeMajor.Rd          |only
 icd9-0.3/icd9/man/icd9ExpandRangeShort.Rd          |   13 
 icd9-0.3/icd9/man/icd9Explain.Rd                   |   18 -
 icd9-0.3/icd9/man/icd9InReferenceCode.Rd           |    8 
 icd9-0.3/icd9/man/icd9InvalidActions.Rd            |only
 icd9-0.3/icd9/man/icd9InvalidDecimal.Rd            |only
 icd9-0.3/icd9/man/icd9IsVE.Rd                      |only
 icd9-0.3/icd9/man/icd9ParentMinor.Rd               |only
 icd9-0.3/icd9/man/icd9PartsRecompose.Rd            |   63 ++-
 icd9-0.3/icd9/man/icd9ShortToDecimal.Rd            |   30 -
 icd9-0.3/icd9/man/icd9ShortToMajor.Rd              |only
 icd9-0.3/icd9/man/icd9ShortToParts.Rd              |    8 
 icd9-0.3/icd9/man/icd9SortShort.Rd                 |    3 
 icd9-0.3/icd9/man/icd9SubsequentMinors.Rd          |    7 
 icd9-0.3/icd9/man/icd9Tell.Rd                      |only
 icd9-0.3/icd9/man/icd9Valid.Rd                     |   16 
 icd9-0.3/icd9/man/icd9ValidDecimal.Rd              |    9 
 icd9-0.3/icd9/man/icd9ValidMajor.Rd                |   16 
 icd9-0.3/icd9/man/icd9ValidMapping.Rd              |   16 
 icd9-0.3/icd9/man/icd9ValidNaWarnStop.Rd           |   38 +-
 icd9-0.3/icd9/man/icd9ValidShort.Rd                |    9 
 icd9-0.3/icd9/man/logicalToBinary.Rd               |    6 
 icd9-0.3/icd9/man/parseIcd9Chapters.Rd             |only
 icd9-0.3/icd9/man/read.zip.url.Rd                  |only
 icd9-0.3/icd9/man/spawnReferenceChildren.Rd        |    2 
 icd9-0.3/icd9/man/stopIfInvalidIcd9.Rd             |   21 -
 icd9-0.3/icd9/man/strip.Rd                         |    2 
 icd9-0.3/icd9/tests/testthat/test-comorbid.R       |   10 
 icd9-0.3/icd9/tests/testthat/test-convert.R        |  221 +++++++++++--
 icd9-0.3/icd9/tests/testthat/test-explain.R        |only
 icd9-0.3/icd9/tests/testthat/test-icd9.R           |  342 +++++++++++----------
 icd9-0.3/icd9/tests/testthat/test-ranges.R         |   21 -
 icd9-0.3/icd9/tests/testthat/test-validation.R     |   21 -
 icd9-0.3/icd9/vignettes/icd9-concordance.tex       |    9 
 icd9-0.3/icd9/vignettes/icd9.Rnw                   |  101 ++++--
 81 files changed, 1288 insertions(+), 633 deletions(-)

More information about icd9 at CRAN
Permanent link

Package clusterSim updated to version 0.43-5 with previous version 0.43-4 dated 2014-02-27

Title: Searching for optimal clustering procedure for a data set
Description: GDM Distance, Sokal-Michener Distance, Bray-Curtis Distance, Calinski-Harabasz Index, G2 Index, G3 Index, Silhouette Index, Krzanowski-Lai Index, Hartigan Index, Gap Index, DB Index, Data Normalization, HINoV method, Replication analysis for cluster validation, Clustering with several algorithms, distances, Symbolic interval distances, Plot functions, Random cluster generation, Linear ordering methods, Comparing partitions, Spectral clustering, Ordinal to metric scale transformation, Untypical data generation.
Author: Marek Walesiak Andrzej Dudek
Maintainer: Andrzej Dudek

Diff between clusterSim versions 0.43-4 dated 2014-02-27 and 0.43-5 dated 2014-07-07

 DESCRIPTION                            |    8 -
 MD5                                    |   20 +-
 R/data.Normalization.r                 |  238 ++++++++++++++++++---------------
 data/data_binary.rda                   |binary
 data/data_interval.rda                 |binary
 data/data_mixed.rda                    |binary
 data/data_nominal.rda                  |binary
 data/data_ordinal.rda                  |binary
 data/data_ratio.rda                    |binary
 inst/doc/dataNormalization_details.pdf |binary
 man/data.Normalization.rd              |    2 
 11 files changed, 147 insertions(+), 121 deletions(-)

More information about clusterSim at CRAN
Permanent link

Package RODBCext updated to version 0.2.2 with previous version 0.2.1 dated 2014-07-03

Title: Parameterized queries extension for RODBC
Description: An extension for RODBC package adding support for parameterized queries
Author: Mateusz Zoltak [aut, cre], Brian Ripley [aut], Michael Lapsley [aut]
Maintainer: Mateusz Zoltak

Diff between RODBCext versions 0.2.1 dated 2014-07-03 and 0.2.2 dated 2014-07-07

 RODBCext |only
 1 file changed

More information about RODBCext at CRAN
Permanent link

New package meteoForecast with initial version 0.31
Package: meteoForecast
Type: Package
Title: Retrieve meteorological forecast from Meteogalicia and OpenMeteo services
Version: 0.31
Date: 2014-07-07
Authors@R: c(person("Oscar", "Perpinan Lamigueiro", email="oscar.perpinan@gmail.com", role=c('cre', 'aut')), person("Marcelo", "Almeida", email= "marcelopa@iee.usp.br", role='ctb'))
Description: Retrieve meteorological forecast from Meteogalicia and OpenMeteo services
URL: http://github.com/oscarperpinan/meteoForecast
License: GPL-3 | file LICENSE
Depends: raster, sp, zoo
Imports: ncdf, rjson
Suggests: ncdf4, rgdal, lattice, rasterVis
Packaged: 2014-07-07 13:17:41 UTC; oscar
Author: Oscar Perpinan Lamigueiro [cre, aut], Marcelo Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-07 15:42:08

More information about meteoForecast at CRAN
Permanent link

Package readODS updated to version 1.4 with previous version 1.3 dated 2014-07-03

Title: Read ODS files and puts them into data frames
Description: Read ODS (OpenDocument Spreadsheet) files and put them into data frames.
Author: Gerrit-Jan Schutten
Maintainer: Gerrit-Jan Schutten

Diff between readODS versions 1.3 dated 2014-07-03 and 1.4 dated 2014-07-07

 DESCRIPTION            |    6 +++---
 MD5                    |   12 ++++++------
 R/readODS.R            |    7 +++++++
 man/getODSRoot.Rd      |    1 +
 man/lettersToNumber.Rd |    1 +
 man/numberToLetters.Rd |    1 +
 man/odsPreParser.Rd    |   18 ++++++++++++++++--
 7 files changed, 35 insertions(+), 11 deletions(-)

More information about readODS at CRAN
Permanent link

Package plotSEMM updated to version 2.0 with previous version 1.0 dated 2008-04-07

Title: Graphing nonlinear latent variable interactions in SEMM
Description: Contains functions plotSEMM_setup, plotSEMM_contour, and plotSEMM_probability, which generate the diagnostic plots proposed by Bauer (2005) to investigate nonlinear latent variable interactions in SEMM using LISREL output.
Author: Bethany Kok [ctb], Jolynn Pek [ctb], Sonya Sterba [ctb], Dan Bauer [ctb], Phil Chalmers [cre, ctb]
Maintainer: Phil Chalmers

Diff between plotSEMM versions 1.0 dated 2008-04-07 and 2.0 dated 2014-07-07

 plotSEMM-1.0/plotSEMM/R/plotSEMM_legend.R         |only
 plotSEMM-1.0/plotSEMM/man/plotSEMM-package.Rd     |only
 plotSEMM-1.0/plotSEMM/man/plotSEMM_legend.Rd      |only
 plotSEMM-2.0/plotSEMM/DESCRIPTION                 |   42 +-
 plotSEMM-2.0/plotSEMM/MD5                         |only
 plotSEMM-2.0/plotSEMM/NAMESPACE                   |only
 plotSEMM-2.0/plotSEMM/R/plotSEMM-package.R        |only
 plotSEMM-2.0/plotSEMM/R/plotSEMM_GUI.R            |only
 plotSEMM-2.0/plotSEMM/R/plotSEMM_ci.R             |only
 plotSEMM-2.0/plotSEMM/R/plotSEMM_contour.R        |  223 ++++++++-----
 plotSEMM-2.0/plotSEMM/R/plotSEMM_probability.R    |  184 +++++++----
 plotSEMM-2.0/plotSEMM/R/plotSEMM_setup.R          |  361 +++++++++++++---------
 plotSEMM-2.0/plotSEMM/R/plotSEMM_setup2.R         |only
 plotSEMM-2.0/plotSEMM/R/read.plotSEMM_wACOV.R     |only
 plotSEMM-2.0/plotSEMM/R/util.R                    |only
 plotSEMM-2.0/plotSEMM/README.md                   |only
 plotSEMM-2.0/plotSEMM/man/plotSEMM.Rd             |only
 plotSEMM-2.0/plotSEMM/man/plotSEMM_GUI.Rd         |only
 plotSEMM-2.0/plotSEMM/man/plotSEMM_contour.Rd     |  120 ++++---
 plotSEMM-2.0/plotSEMM/man/plotSEMM_probability.Rd |  111 +++---
 plotSEMM-2.0/plotSEMM/man/plotSEMM_setup.Rd       |  119 +++----
 plotSEMM-2.0/plotSEMM/src                         |only
 22 files changed, 710 insertions(+), 450 deletions(-)

More information about plotSEMM at CRAN
Permanent link

Package muscle updated to version 3.8.31-4 with previous version 3.8.31-3 dated 2014-07-04

Title: Multiple Sequence Alignment
Description: MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.
Author: Algorithm by Robert C. Edgar. R port by Alex T. Kalinka.
Maintainer: Alex T. Kalinka

Diff between muscle versions 3.8.31-3 dated 2014-07-04 and 3.8.31-4 dated 2014-07-07

 DESCRIPTION          |    6 +++---
 MD5                  |    4 ++--
 src/globalslinux.cpp |    9 ++++++++-
 3 files changed, 13 insertions(+), 6 deletions(-)

More information about muscle at CRAN
Permanent link

New package MCAvariants with initial version 1.0
Package: MCAvariants
Type: Package
Title: Multiple Correspondence Analysis Variants
Version: 1.0
Date: 2014-06-27
Author: Rosaria Lombardo
Maintainer: Rosaria Lombardo
Description: Classical multiple correspondence analysis and multiple correspondence analysis via orthogonal polynomials
Depends: methods
License: GPL
Packaged: 2014-07-07 08:05:16 UTC; utente
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-07 11:57:28

More information about MCAvariants at CRAN
Permanent link

Package LSAfun updated to version 0.3.1 with previous version 0.3 dated 2014-06-25

Title: Applied Latent Semantic Analysis (LSA) functions
Description: This package provides functions that allow for convenient working with Latent Semantic Analysis. For actually building an LSA space, use the package 'lsa'.
Author: Fritz Guenther [aut, cre]
Maintainer: Fritz Guenther

Diff between LSAfun versions 0.3 dated 2014-06-25 and 0.3.1 dated 2014-07-07

 LSAfun-0.3.1/LSAfun/ChangeLog             |   15 +++++++++-
 LSAfun-0.3.1/LSAfun/DESCRIPTION           |    6 ++--
 LSAfun-0.3.1/LSAfun/MD5                   |   43 +++++++++++++++++-------------
 LSAfun-0.3.1/LSAfun/NAMESPACE             |    4 +-
 LSAfun-0.3.1/LSAfun/R/Predication.r       |    8 ++---
 LSAfun-0.3.1/LSAfun/R/genericSummary.R    |    1 
 LSAfun-0.3.1/LSAfun/R/neighbors.r         |only
 LSAfun-0.3.1/LSAfun/R/plot_neighbors.r    |only
 LSAfun-0.3.1/LSAfun/R/plot_wordlist.r     |    9 ++++--
 LSAfun-0.3.1/LSAfun/data/datalist         |only
 LSAfun-0.3.1/LSAfun/data/oldbooks.rda     |only
 LSAfun-0.3.1/LSAfun/data/priming.rda      |only
 LSAfun-0.3.1/LSAfun/data/syntest.rda      |only
 LSAfun-0.3.1/LSAfun/data/wonderland.rda   |binary
 LSAfun-0.3.1/LSAfun/man/LSAfun-package.Rd |    2 -
 LSAfun-0.3.1/LSAfun/man/Predication.Rd    |   14 ++++-----
 LSAfun-0.3.1/LSAfun/man/choose.target.Rd  |    2 -
 LSAfun-0.3.1/LSAfun/man/compose.Rd        |    2 -
 LSAfun-0.3.1/LSAfun/man/costring.Rd       |    2 -
 LSAfun-0.3.1/LSAfun/man/multicostring.Rd  |    4 +-
 LSAfun-0.3.1/LSAfun/man/neighbors.Rd      |only
 LSAfun-0.3.1/LSAfun/man/oldbooks.Rd       |only
 LSAfun-0.3.1/LSAfun/man/plot_neighbors.Rd |only
 LSAfun-0.3.1/LSAfun/man/plot_wordlist.Rd  |    9 +++---
 LSAfun-0.3.1/LSAfun/man/priming.Rd        |only
 LSAfun-0.3.1/LSAfun/man/syntest.Rd        |only
 LSAfun-0.3/LSAfun/R/neighbours.r          |only
 LSAfun-0.3/LSAfun/R/plot_neighbours.r     |only
 LSAfun-0.3/LSAfun/man/neighbours.Rd       |only
 LSAfun-0.3/LSAfun/man/plot_neighbours.Rd  |only
 30 files changed, 73 insertions(+), 48 deletions(-)

More information about LSAfun at CRAN
Permanent link

Package CoClust updated to version 0.3-0 with previous version 0.2-9 dated 2013-06-24

Title: Copula based cluster analysis
Description: Copula based cluster analysis.
Author: Francesca Marta Lilja Di Lascio, Simone Giannerini
Maintainer: Simone Giannerini

Diff between CoClust versions 0.2-9 dated 2013-06-24 and 0.3-0 dated 2014-07-07

 CoClust-0.2-9/CoClust/ChangeLog.txt          |only
 CoClust-0.3-0/CoClust/ChangeLog              |only
 CoClust-0.3-0/CoClust/DESCRIPTION            |   11 
 CoClust-0.3-0/CoClust/MD5                    |   16 
 CoClust-0.3-0/CoClust/NAMESPACE              |    5 
 CoClust-0.3-0/CoClust/R/CoClust.R            |  491 ++++++++-------------------
 CoClust-0.3-0/CoClust/R/Internal_functions.R |  149 ++------
 CoClust-0.3-0/CoClust/inst/CITATION          |    6 
 CoClust-0.3-0/CoClust/man/CoClust-class.Rd   |    4 
 CoClust-0.3-0/CoClust/man/CoClust.Rd         |   24 -
 10 files changed, 240 insertions(+), 466 deletions(-)

More information about CoClust at CRAN
Permanent link

Package rLakeAnalyzer updated to version 1.4 with previous version 1.3 dated 2014-02-07

Title: Package for the analysis of lake physics
Description: Standardized methods for calculating common important derived physical features of lakes including water density based based on temperature, thermal layers, thermocline depth, lake number, Wedderburn number, Schmidt stability and others.
Author: Luke Winslow, Jordan Read, Richard Woolway, Jennifer Brentrup, Taylor Leach, Jake Zwart
Maintainer: Luke Winslow

Diff between rLakeAnalyzer versions 1.3 dated 2014-02-07 and 1.4 dated 2014-07-07

 rLakeAnalyzer-1.3/rLakeAnalyzer/R/test.R                            |only
 rLakeAnalyzer-1.3/rLakeAnalyzer/inst/extdata/gFileOpen.m            |only
 rLakeAnalyzer-1.3/rLakeAnalyzer/inst/extdata/gFileSave.m            |only
 rLakeAnalyzer-1.3/rLakeAnalyzer/inst/extdata/gPivot.m               |only
 rLakeAnalyzer-1.3/rLakeAnalyzer/inst/extdata/misc.asv               |only
 rLakeAnalyzer-1.3/rLakeAnalyzer/inst/extdata/misc.m                 |only
 rLakeAnalyzer-1.3/rLakeAnalyzer/inst/extdata/timeseriesaggregator.m |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/DESCRIPTION                         |    9 
 rLakeAnalyzer-1.4/rLakeAnalyzer/MD5                                 |   39 ++--
 rLakeAnalyzer-1.4/rLakeAnalyzer/NAMESPACE                           |    7 
 rLakeAnalyzer-1.4/rLakeAnalyzer/R/lake.number.plot.R                |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/R/load.data.R                       |   13 +
 rLakeAnalyzer-1.4/rLakeAnalyzer/R/schmidt.plot.R                    |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/R/timeseries.functions.R            |   97 ++++++++--
 rLakeAnalyzer-1.4/rLakeAnalyzer/R/wtr.heatmap.layers.R              |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/R/wtr.lineseries.R                  |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/R/wtr.plot.temp.R                   |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/README.md                           |    1 
 rLakeAnalyzer-1.4/rLakeAnalyzer/build                               |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/inst/doc                            |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/man/lake.number.plot.Rd             |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/man/load.bathy.Rd                   |    2 
 rLakeAnalyzer-1.4/rLakeAnalyzer/man/load.ts.Rd                      |    6 
 rLakeAnalyzer-1.4/rLakeAnalyzer/man/schmidt.plot.Rd                 |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/man/ts.layer.temperature.Rd         |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/man/ts.meta.depths.Rd               |   12 -
 rLakeAnalyzer-1.4/rLakeAnalyzer/man/wtr.heatmap.layers.Rd           |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/man/wtr.lineseries.Rd               |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/man/wtr.plot.temp.Rd                |only
 rLakeAnalyzer-1.4/rLakeAnalyzer/vignettes                           |only
 30 files changed, 141 insertions(+), 45 deletions(-)

More information about rLakeAnalyzer at CRAN
Permanent link

New package ONETr with initial version 0.1-1
Package: ONETr
Type: Package
Title: Efficient authenticated interaction with the O*NET API.
Version: 0.1-1
Date: 2014-06-18
Author: Eric Knudsen
Maintainer: Eric Knudsen
Description: This package provides a series of functions designed to enable users to easily search and interact with occupational data from the O*NET API . The package produces parsed and listed XML data for custom interactions, or pre-packaged functions for easy extraction of specific data (e.g., Knowledge, Skills, Abilities, Work Styles, etc.).
Depends: XML, RCurl
License: GPL-3
Packaged: 2014-07-07 06:10:36 UTC; ripley
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-07 08:12:39

More information about ONETr at CRAN
Permanent link


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