CRANberries

Thu, 31 Jan 2013

Package taxize updated to version 0.0.4 with previous version 0.0.3 dated 2013-01-30

Title: Taxonomic information from around the web.
Description: Taxonomic information from around the web.
Author: Scott Chamberlain [aut, cre], Eduard Szoecs [aut], Carl Boettiger [aut], Ignasi Bartomeus [aut]
Maintainer: Scott Chamberlain

Diff between taxize versions 0.0.3 dated 2013-01-30 and 0.0.4 dated 2013-01-31 

 taxize-0.0.3/taxize/CONTRIBUTING.md                 |only
 taxize-0.0.3/taxize/inst/tests/test-ubio_namebank.R |only
 taxize-0.0.4/taxize/DESCRIPTION                     |    9 ++--
 taxize-0.0.4/taxize/MD5                             |   12 ++---
 taxize-0.0.4/taxize/NEWS                            |    7 +++
 taxize-0.0.4/taxize/R/tnrs.R                        |   44 ++++++++++++++------
 taxize-0.0.4/taxize/inst/tests/test-tnrs.R          |    2 
 taxize-0.0.4/taxize/man/tnrs.Rd                     |   22 +++++++---
 8 files changed, 67 insertions(+), 29 deletions(-)

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Package MissingDataGUI updated to version 0.1-5 with previous version 0.1-4 dated 2013-01-30

Title: A GUI for Missing Data Exploration
Description: This package provides numeric and graphical summaries for the missing values from both discrete and continuous variables. A variety of imputation methods are applied, including univariate imputations like fixed or random values, multiple imputations based on other packages, and imputations conditioned on a categorical variable.
Author: Xiaoyue Cheng, Dianne Cook, Heike Hofmann
Maintainer: Xiaoyue Cheng

Diff between MissingDataGUI versions 0.1-4 dated 2013-01-30 and 0.1-5 dated 2013-01-31 

 DESCRIPTION               |    8 ++++----
 MD5                       |    6 +++---
 R/WatchMissingValues.r    |    3 ++-
 inst/doc/introduction.pdf |binary
 4 files changed, 9 insertions(+), 8 deletions(-)

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Package argparse updated to version 0.5.2 with previous version 0.5.0 dated 2013-01-29

Title: Command line optional and positional argument parser.
Description: A command line parser to be used with Rscript to write "#!" shebang scripts that gracefully accept positional and optional arguments and automatically generate usage. Initial beta release.
Author: Trevor L Davis. Ports examples from the argparse Python module by the Python Software Foundation. Ports examples from the getopt package by Allen Day.
Maintainer: Trevor L Davis

Diff between argparse versions 0.5.0 dated 2013-01-29 and 0.5.2 dated 2013-01-31 

 DESCRIPTION                |    6 +++---
 MD5                        |    8 ++++----
 R/argparse.R               |   25 +++++++++++++++++--------
 inst/doc/argparse.pdf      |binary
 inst/tests/test-argparse.R |    1 +
 5 files changed, 25 insertions(+), 15 deletions(-)

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New package Ritc with initial version 1.0.0
Package: Ritc
Type: Package
Title: Isothermal Titration Calorimetry (ITC) Data Analysis
Version: 1.0.0
Author: Yingyun Liu
Maintainer: Yingyun Liu
Depends: minpack.lm
Description: This package implements the simulation and regression of integrated Isothermal Titration Calorimetry (ITC) data using the most commonly used one-to-one binding reaction model.
License: GPL (>= 2)
Packaged: 2013-01-31 19:50:38 UTC; Liu
Repository: CRAN
Date/Publication: 2013-01-31 21:05:57

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Package Cubist updated to version 0.0.13 with previous version 0.0.12 dated 2012-02-29

Title: Rule- and Instance-Based Regression Modeling
Description: Regression modeling using rules with added instance-based corrections
Author: Max Kuhn, Steve Weston, Chris Keefer, Nathan Coulter. C code for Cubist by Ross Quinlan
Maintainer: Max Kuhn

Diff between Cubist versions 0.0.12 dated 2012-02-29 and 0.0.13 dated 2013-01-31 

 DESCRIPTION         |    8 ++++----
 MD5                 |   12 ++++++------
 R/lattice.R         |    5 +++++
 R/makeDataFile.R    |   22 +++++++++++++---------
 R/makeNamesFile.R   |   38 +++++++++++++++++++++++++++++++++++++-
 inst/NEWS.Rd        |   13 +++++++++++++
 inst/doc/cubist.pdf |binary
 7 files changed, 78 insertions(+), 20 deletions(-)

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Package vimcom updated to version 0.9-7 with previous version 0.9-5 dated 2012-12-02

Title: Intermediate the communication between Vim and R
Description: Provide a service to intermediate the communication between Vim and R.
Author: Jakson Aquino
Maintainer: Jakson Alves de Aquino

Diff between vimcom versions 0.9-5 dated 2012-12-02 and 0.9-7 dated 2013-01-31 

 DESCRIPTION     |   10 --
 MD5             |   14 +--
 NEWS            |   12 ++
 README          |    2 
 configure       |   18 ++--
 configure.ac    |    2 
 src/vimcom.c    |  245 +++++++++++++++++++++++++++++++++++++++++++++++---------
 src/vimremote.c |    1 
 8 files changed, 243 insertions(+), 61 deletions(-)

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New package Sequential with initial version 1.0
Package: Sequential
Type: Package
Title: Exact Sequential Analysis for Poisson Data
Version: 1.0
Date: 2012-11-14
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva
Description: Calculates exact critical values to perform continuous or group sequential analysis for Poisson type data using the Maximized Sequential Probability Ratio Test (MaxSPRT) with a Wald type rejection boundary. Also calculates properties such as statistical power, expected time to signal when the null is rejected and maximum sample size needed to obtain a certain power.
License: GPL-2
LazyLoad: yes
Packaged: 2013-01-30 16:39:15 UTC; Ivair
Repository: CRAN
Date/Publication: 2013-01-31 15:54:25

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Package postCP updated to version 1.6.3 with previous version 1.6.2 dated 2012-12-21

Title: A package to estimate posterior probabilities and perform model selection in change-point models using constrained HMM.
Description: The functions are used for change-point problems, after an initial set of change-points within the data has already been obtained. The function postCP obtains estimates of posterior probabilities of change-point and hidden states for each observation, and confidence intervals for the positions of the change-point. The function postCPsample obtains random samples of sets of change-points using the output of the postCP function. Model selection may be performed using function postCPmodelsel through criteria obtained from function postCPcrit.
Author: Gregory Nuel and The Minh Luong
Maintainer: The Minh Luong

Diff between postCP versions 1.6.2 dated 2012-12-21 and 1.6.3 dated 2013-01-31 

 DESCRIPTION           |    8 +++----
 MD5                   |   22 ++++++++++-----------
 R/postCP.r            |   51 +++++++++++++++++++++++++++++++-------------------
 man/GreedySegmente.Rd |    4 +--
 man/lesum.Rd          |    4 +--
 man/mleNB.Rd          |    6 ++---
 man/plot.postCP.Rd    |    4 +--
 man/postCP.Rd         |   12 +++++------
 man/postCPcrit.Rd     |    4 +--
 man/postCPmodelsel.Rd |    4 +--
 man/postCPsample.Rd   |    6 ++---
 man/viterbi.Rd        |    4 +--
 12 files changed, 71 insertions(+), 58 deletions(-)

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Package hash updated to version 2.2.5 with previous version 2.2.4 dated 2012-10-29

Title: Full feature implementation of hash/associated arrays/dictionaries
Description: This package implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor. For objects of appreciable size, access using hashes outperforms native named lists and vectors.
Author: Christopher Brown
Maintainer: Christopher Brown

Diff between hash versions 2.2.4 dated 2012-10-29 and 2.2.5 dated 2013-01-31 

 ChangeLog           |    7 +++++--
 DESCRIPTION         |    8 ++++----
 MD5                 |   11 ++++++-----
 R/Class-hash.R      |   12 ++++++------
 R/has-key.R         |    2 +-
 man/hash-package.Rd |    4 ++--
 tests/has.key.R     |only
 7 files changed, 24 insertions(+), 20 deletions(-)

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Package gWidgetstcltk updated to version 0.0-54 with previous version 0.0-53 dated 2012-10-09

Title: Toolkit implementation of gWidgets for tcltk package
Description: Port of the gWidgets API to the tcltk package. Requires TK 8.5 or greater for the tile (ttk)widgets http://www.tcl.tk/software/tcltk/8.5.tml. This is the default on Windows. Under linux, Tk must be installed. Under Mac OS X (10.5) there are two options: native Tk or X11. For the native one, Tk must be upgraded. See www.tcl.tk to download source. Under the Mac it compiles and installs cleanly. For X11, tcltk libraries can be downloaded to augment the R binary package. See http://cran.r-project.org/bin/macosx/tools/. The gdf function requires the add on Tk package TkTable (http://tktable.sourceforge.net/).
Author: John Verzani
Maintainer: John Verzani

Diff between gWidgetstcltk versions 0.0-53 dated 2012-10-09 and 0.0-54 dated 2013-01-31 

 DESCRIPTION |    6 +++---
 MD5         |    8 ++++----
 NEWS        |    6 ++++++
 R/gfile.R   |    9 +++++++++
 R/gslider.R |    6 +++---
 5 files changed, 25 insertions(+), 10 deletions(-)

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New package dvn with initial version 0.1
Package: dvn
Version: 0.1
Date: 2013-01-30
Title: Access to The Dataverse Network API
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper
Depends: bitops, RCurl, XML
Description: Provides access to The Dataverse Network API via the RCurl package, enabling access to archived data (and metadata), along with a number of functions to translate responses to API calls into R data structures using the XML package.
License: GPL-2
URL: http://thomasleeper.com/software.html
Packaged: 2013-01-31 10:29:17 UTC; Thomas
Repository: CRAN
Date/Publication: 2013-01-31 15:54:27

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Package Devore7 updated to version 0.7.5 with previous version 0.7.4 dated 2011-11-05

Title: Data sets from Devore's "Prob and Stat for Eng (7th ed)"
Description: Data sets and sample analyses from Jay L. Devore (2008), "Probability and Statistics for Engineering and the Sciences (7th ed)", Thomson.
Author: Original by Jay L. Devore, modifications by Douglas Bates , modifications for 7th edition by John Verzani.
Maintainer: John Verzani

Diff between Devore7 versions 0.7.4 dated 2011-11-05 and 0.7.5 dated 2013-01-31 

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Permanent link

Package CBPS updated to version 0.3 with previous version 0.2 dated 2012-09-29

Title: R Package for Covariate Balancing Propensity Score
Description: CBPS is an R package that implements the covariate balancing propensity score proposed by Imai and Ratkovic (2012). The propensity score is estimated such that it maximizes the resulting covariate balance as well as the prediction of treatment assignment. The method, therefore, avoids an iteration between model fitting and balance checking. Currently, the package can only deal with binary treatment in the cross section setting but in the future it will be extended to other settings including non-binary treatments and causal inference with longitudinal data.
Author: Marc Ratkovic , Kosuke Imai , Christian Fong
Maintainer: Marc Ratkovic

Diff between CBPS versions 0.2 dated 2012-09-29 and 0.3 dated 2013-01-31 

 ChangeLog        |    1 
 DESCRIPTION      |    8 +-
 MD5              |   12 ++--
 R/CovarBalFunc.R |  152 +++++++++++++++++++++++++++++++++++++------------------
 man/CBPS.Rd      |    9 +--
 man/DR.rd        |    3 +
 man/IPW.Rd       |    3 -
 7 files changed, 126 insertions(+), 62 deletions(-)

More information about CBPS at CRAN
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New package BH with initial version 1.51.0-0
Package: BH
Type: Package
Title: The Boost C++ Libraries
Version: 1.51.0-0
Date: 2013-01-29
Author: John W. Emerson, Michael J. Kane, Dirk Eddelbuettel, JJ Allaire, and Romain Francois
Maintainer: Jay Emerson
Description: Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN package. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided.
License: BSL-1.0
Packaged: 2013-01-31 14:05:39 UTC; jay
Repository: CRAN
Date/Publication: 2013-01-31 15:54:23

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New package ForImp with initial version 1.0.2
Package: ForImp
Type: Package
Title: Imputation of missing values through a forward imputation algorithm
Version: 1.0.2
Date: 2013-01-30
Author: Alessandro Barbiero, Pier Alda Ferrari, Giancarlo Manzi
Maintainer: Alessandro Barbiero
Description: Imputation of missing values in datasets of ordinal variables through a forward imputation algorithm
License: GPL
LazyLoad: yes
Depends: homals, sampling, mvtnorm
Packaged: 2013-01-31 07:46:46 UTC; Alessandro
Repository: CRAN
Date/Publication: 2013-01-31 11:05:58

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Package BiodiversityR updated to version 2.1 with previous version 2.0 dated 2012-12-19

Title: GUI for biodiversity, suitability and community ecology analysis
Description: This package provides a GUI (Graphical User Interface, via the R-Commander) and some utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt

Diff between BiodiversityR versions 2.0 dated 2012-12-19 and 2.1 dated 2013-01-31 

 DESCRIPTION                  |   18 ++---
 MD5                          |   12 +--
 NAMESPACE                    |    4 +
 R/BiodiversityRGUI.R         |    2 
 inst/etc/BiodiversityGUI.R   |   32 +++++-----
 man/BiodiversityR-package.Rd |    2 
 man/BiodiversityRGUI.Rd      |  130 +------------------------------------------
 7 files changed, 42 insertions(+), 158 deletions(-)

More information about BiodiversityR at CRAN
Permanent link

Package splinesurv (with last version 0.6-14) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2010-07-31 0.6-14
2010-07-28 0.6-13

Permanent link
Package iDEMO (with last version 0.2-01) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2012-06-06 0.2-01
2012-04-29 0.2-0

Permanent link
Package mixOmics (with last version 4.0-2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2012-05-31 4.0-2
2012-04-06 4.0-1
2011-08-11 3.0
2011-06-23 2.9-6
2011-03-18 2.9-4
2011-01-27 2.9-2
2010-11-08 2.9-1
2010-08-12 2.8-1
2010-05-28 2.7-1
2010-02-25 2.6

Permanent link
Package ReadImages (with last version 0.1.3.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2012-12-21 0.1.3.3
2012-04-19 0.1.3.2
2009-07-30 0.1.3.1
2009-07-27 0.1.3
2009-05-27 0.1.2
2009-05-19 0.1.1

Permanent link
Package integrativeME (with last version 1.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2010-03-05 1.2
2009-10-14 1.1

Permanent link
Package SNPRelate updated to version 0.9.11 with previous version 0.9.10 dated 2013-01-21

Title: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)
Description: A High-performance computing toolset for relatedness and principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng

Diff between SNPRelate versions 0.9.10 dated 2013-01-21 and 0.9.11 dated 2013-01-31 

 DESCRIPTION                     |   10 -
 MD5                             |   96 ++++++++---------
 NEWS                            |    9 +
 R/main.r                        |  130 ++++++++++++------------
 inst/doc/SNPRelateTutorial.Rnw  |  216 +++++++++++++++++++++++++++++++++-------
 inst/doc/SNPRelateTutorial.pdf  |binary
 inst/extdata/hapmap_geno.gds    |binary
 man/SNPRelate-package.Rd        |    4 
 man/snpgdsCombineGeno.Rd        |    4 
 man/snpgdsCreateGeno.Rd         |   10 -
 man/snpgdsCreateGenoSet.Rd      |    4 
 man/snpgdsDiss.Rd               |    2 
 man/snpgdsGDS2BED.Rd            |    2 
 man/snpgdsGDS2Eigen.Rd          |    2 
 man/snpgdsGDS2PED.Rd            |    2 
 man/snpgdsGetGeno.Rd            |    6 -
 man/snpgdsIBDMLE.Rd             |    2 
 man/snpgdsIBDMLELogLik.Rd       |    2 
 man/snpgdsIBDMoM.Rd             |    2 
 man/snpgdsIBS.Rd                |    2 
 man/snpgdsIBSNum.Rd             |    2 
 man/snpgdsIndInb.Rd             |    2 
 man/snpgdsLDMat.Rd              |    2 
 man/snpgdsLDpruning.Rd          |    2 
 man/snpgdsOption.Rd             |    2 
 man/snpgdsPCA.Rd                |   15 +-
 man/snpgdsPCACorr.Rd            |    2 
 man/snpgdsPCASNPLoading.Rd      |    2 
 man/snpgdsPCASampLoading.Rd     |    2 
 man/snpgdsSNPList.Rd            |    2 
 man/snpgdsSNPRateFreq.Rd        |    2 
 man/snpgdsSampMissrate.Rd       |    2 
 man/snpgdsSelectSNP.Rd          |    2 
 man/snpgdsSummary.Rd            |    2 
 src/CoreDEF.h                   |    4 
 src/CoreGDSLink.cpp             |   60 +++++++----
 src/CoreGDSLink.h               |   37 ++++--
 src/dGWASMath.h                 |    2 
 src/dGenGWAS.cpp                |    4 
 src/dGenGWAS.h                  |    8 -
 src/dType.h                     |  171 +++++++++++++++++++++++++++++--
 src/dVect.cpp                   |    2 
 src/dVect.h                     |    4 
 src/genIBD.cpp                  |   18 +--
 src/genIBS.cpp                  |   18 +--
 src/genLD.cpp                   |   18 +--
 src/genPCA.cpp                  |   18 +--
 src/main.cpp                    |   31 ++---
 vignettes/SNPRelateTutorial.Rnw |  216 +++++++++++++++++++++++++++++++++-------
 49 files changed, 820 insertions(+), 337 deletions(-)

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New package modiscloud with initial version 0.13
Package: modiscloud
Type: Package
Title: R tools for processing Level 2 Cloud Mask products from MODIS
Version: 0.13
Date: 2013-01-30
Author: Nicholas J. Matzke, Dept. of Integrative Biology, U.C. Berkeley
Maintainer: Nicholas J. Matzke
Depends: date, sp, sfsmisc, raster, rgdal
Description: Package for processing downloaded MODIS cloud product HDF files and derived files. Specifically, MOD35_L2 cloud product files, and the associated MOD03 geolocation files (for MODIS-TERRA); and MYD35_L2 cloud product files, and the associated MYD03 geolocation files (for MODIS-AQUA). The package will be most effective if the user installs MRTSwath (MODIS Reprojection Tool for swath products; https://lpdaac.usgs.gov/tools/modis_reprojection_tool_swath), and adds the directory with the MRTSwath executable to the default R PATH by editing ~/.Rprofile.
License: GPL
ByteCompile: true
Packaged: 2013-01-30 22:45:25 UTC; nickm
Repository: CRAN
Date/Publication: 2013-01-31 08:11:52

More information about modiscloud at CRAN
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Package daewr updated to version 1.0-3 with previous version 1.0-1 dated 2012-11-17

Title: Design and Analysis of Experiments with R
Description: This package contains data frames and functions used in the book "Design and Analysis of Experiments with R"
Author: John Lawson
Maintainer: John Lawson

Diff between daewr versions 1.0-1 dated 2012-11-17 and 1.0-3 dated 2013-01-31 

 DESCRIPTION        |   11 ++++++-----
 MD5                |   46 +++++++++++++++++++++++++++++++++++++---------
 NAMESPACE          |    4 +++-
 R/Altscreen.R      |   23 ++++++++++++-----------
 R/ModelRobust.R    |only
 R/OptPB.R          |only
 data/MR12m5g5.rda  |only
 data/MR12m6g5.rda  |only
 data/MR12m7g4.rda  |only
 data/MR12m8g3.rda  |only
 data/MR12m9g2.rda  |only
 data/MR16m10g3.rda |only
 data/MR16m7g5.rda  |only
 data/MR16m8g5.rda  |only
 data/MR16m9g5.rda  |only
 data/MR8m4g3.rda   |only
 data/MR8m5g2.rda   |only
 data/MR8m6g1.rda   |only
 man/Altscreen.Rd   |   28 +++++++++++++---------------
 man/LGB.Rd         |    1 -
 man/MR12m5g5.Rd    |only
 man/MR12m6g5.Rd    |only
 man/MR12m7g4.Rd    |only
 man/MR12m8g3.Rd    |only
 man/MR12m9g2.Rd    |only
 man/MR16m10g3.Rd   |only
 man/MR16m7g5.Rd    |only
 man/MR16m8g5.Rd    |only
 man/MR16m9g5.Rd    |only
 man/MR8m4g3.Rd     |only
 man/MR8m5g2.Rd     |only
 man/MR8m6g1.Rd     |only
 man/ModelRobust.Rd |only
 man/OptPB.Rd       |only
 man/Tukey1df.Rd    |    6 +++---
 man/bioequiv.Rd    |    2 +-
 man/bioeqv.Rd      |    4 ++--
 man/chipman.Rd     |    2 +-
 38 files changed, 78 insertions(+), 49 deletions(-)

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New package ALKr with initial version 0.5
Package: ALKr
Type: Package
Title: Generate Age-Length Keys for fish populations
Description: A collection of functions that implement several algorithms for generating age-length keys for fish populations from incomplete data.
URL: http://www.github.com/ALKr
Version: 0.5
Date: 2013-01-30
Author: Jose Francisco Loff, Alberto Murta, Laurence Kell
Maintainer: Jose Francisco Loff
Depends: R (>= 2.15.2), Rcpp (>= 0.10.2)
LinkingTo: Rcpp
Imports: MASS, methods
License: BSD
Collate: 'ALKr.r' 'gascuel.r' 'hoenig.r' 'hoenig_heisey.r' 'inverse_ALK.r' 'kimura_chikuni.r' 'package.r' 'calc_invALK.r' 'calc_ALK.r' 'classic_ALK.r' 'hom.r' 'RcppExports.R' 'age_slicing.r' 'summary.ALKr.r' 'summary_ALKr.r'
Packaged: 2013-01-30 22:31:58 UTC; zeloff
Repository: CRAN
Date/Publication: 2013-01-31 08:01:45

More information about ALKr at CRAN
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