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Revision 48 - Directory Listing
Modified Mon Nov 9 06:07:43 2015 UTC (19 months, 2 weeks ago) by anpefi
Changed DOI specification in CITATION as suggested by CRAN. 

Revision 47 - Directory Listing
Modified Tue Nov 4 07:41:26 2014 UTC (2 years, 7 months ago) by anpefi
CSV file with PCoA coordinates now show all the axes for downstream analyses. This could produce some Warnings if there are eigenvalues = 0.

Revision 46 - Directory Listing
Modified Thu Sep 4 06:58:09 2014 UTC (2 years, 9 months ago) by anpefi
Solved a bug caused by argument checking of subset() within diffAmova() when  do.pairwisePhiST=TRUE as reported by Eamonn B. Mallon

Revision 45 - Directory Listing
Modified Thu May 8 14:21:58 2014 UTC (3 years, 1 month ago) by anpefi
Fixing some typos in the User's Guide

Revision 44 - Directory Listing
Modified Thu May 8 14:16:47 2014 UTC (3 years, 1 month ago) by anpefi
Updated User's Guide pdf to the last version

Revision 43 - Directory Listing
Modified Thu May 8 11:37:57 2014 UTC (3 years, 1 month ago) by anpefi
Truncated /usage and /example lines in msap.Rd to fit to 90 and 100 character width required by R CMD check --as-cran. This revision will be uploaded to CRAN as version 1.1.8.

Revision 42 - Directory Listing
Modified Wed May 7 16:42:41 2014 UTC (3 years, 1 month ago) by anpefi
Tagged as 1.1.8. Removed dependeces to cba, scrime and pegas. PCoA is now performed using dist()  and cmdscale() from package stats. This yields the same PCoA coordinate pattern although with different scale, so numbers seem different. Candidate version to be uploaded to CRAN

Revision 41 - Directory Listing
Modified Tue May 6 11:24:43 2014 UTC (3 years, 1 month ago) by anpefi
Tagged as version 1.1.7
Removed dependeces to pegas and cba. 
do.pairwisePhiST=FALSE by default.
Skip analyses if available loci are less than 2.
Added rainbow color schema to avoid crashes if number of populations is above 8.

Revision 40 - Directory Listing
Modified Wed Mar 13 23:02:07 2013 UTC (4 years, 3 months ago) by anpefi
Minor changes in the vignette. Updating and uploading the pdf manual for version 1.1.6

Revision 39 - Directory Listing
Modified Fri Mar 8 17:30:52 2013 UTC (4 years, 3 months ago) by anpefi
Added BugReports URL in DESCRIPTION

Revision 38 - Directory Listing
Modified Fri Mar 8 17:07:58 2013 UTC (4 years, 3 months ago) by anpefi
Solving an error stoping msap when running aflp analysis with odd number of samples, due to the check of enzymes in datafile. Removed some summy error reports when running aflp analysis.

Revision 37 - Directory Listing
Modified Mon Mar 4 09:33:19 2013 UTC (4 years, 3 months ago) by anpefi
updating DESCRIPTION to version 1.1.5

Revision 36 - Directory Listing
Modified Mon Mar 4 09:22:50 2013 UTC (4 years, 3 months ago) by anpefi
Fixed an error causing that both transformed files were identical for MSL and NML

Revision 35 - Directory Listing
Modified Tue Feb 19 16:57:01 2013 UTC (4 years, 4 months ago) by anpefi
Added dependence to R(>= 2.14.0) as there was some problems in previous versions

Revision 34 - Directory Listing
Modified Mon Feb 11 14:54:21 2013 UTC (4 years, 4 months ago) by anpefi
Added returning of the MSAP patterns matrices

Revision 33 - Directory Listing
Modified Sun Feb 10 02:16:27 2013 UTC (4 years, 4 months ago) by anpefi
Solving a compatibility to R<2.15 issue: calls to paste0 were changed to paste(..,sep="") again. 

Revision 32 - Directory Listing
Modified Thu Feb 7 19:06:26 2013 UTC (4 years, 4 months ago) by anpefi
Changed the dependecy to the amova function in pegas to avoid its feature to get the data from the global environment. Removed assignments of variables into the global environment to meet the CRAN policy.
Added a returning list for the main msap funtion to export transformed data and distance matrices to the global environment for further analysis from the user. 
Changed the codification of states when using use.bands=h to match the codification with those in use.bands=u -> 0: unmethylated, 1:methylated. Results of current analysis are not affected by this change.
Some minor fixes.

Revision 31 - Directory Listing
Modified Wed Feb 6 19:17:21 2013 UTC (4 years, 4 months ago) by anpefi
Bug fixed:  there was an error in the code that consider as polymophic those with more than two occurrences of both states instead of those with at leasr two occurrences. Added: some checkings of data file to diagnose possible problems. Citation information.
Minor changes: estetic changes in the text report. Now it displays name of the files as they are being created.

Revision 30 - Directory Listing
Modified Wed Nov 14 14:15:34 2012 UTC (4 years, 7 months ago) by anpefi
New minor version: 1.1.0. Changes proposed by the reviewers of the MS sent to MER. Major feature: Fragment classification is now done for each primer combination independently. New parameter: no.bands sustitutes uninformative. New parameters: loci.per.primer and error.rate.primer. New feature: saving transformed matrices as csv. methStatusEval rewritten. Changes in the manual: new FAQ. Several minor changes.

Revision 29 - Directory Listing
Modified Tue Oct 9 14:51:07 2012 UTC (4 years, 8 months ago) by anpefi
Added FAQ section into the manual. Manual updated

Revision 28 - Directory Listing
Modified Thu Oct 4 15:41:16 2012 UTC (4 years, 8 months ago) by anpefi
Fixed bug causing crash when no NML were found on the datafile. Added examples to msap.Rd

Revision 27 - Directory Listing
Modified Tue Sep 11 18:47:43 2012 UTC (4 years, 9 months ago) by anpefi
Added export of csv files with data from PCoA (coordinates and eigenvalues) to be externally analysed by users

Revision 26 - Directory Listing
Modified Thu Sep 6 09:05:00 2012 UTC (4 years, 9 months ago) by anpefi
fixed misspeling in DESCRIPTION. User's guide updated.

Revision 25 - Directory Listing
Modified Wed Sep 5 15:11:01 2012 UTC (4 years, 9 months ago) by anpefi
Version 1.0 defined. Several changes from last commit, including Mantel test and fixing of the AFLP mode and minor bugs. I think this version is quite stable.

Revision 23 - Directory Listing
Modified Thu Jul 5 17:58:02 2012 UTC (4 years, 11 months ago) by anpefi
Correction of misspellings in vignette reported by D. Anastasiadi

Revision 22 - Directory Listing
Modified Thu Jul 5 09:27:30 2012 UTC (4 years, 11 months ago) by anpefi
Changed, in web and vignette, instruction to install package from R-Forge, as it was incomplete and caused problems in Windows

Revision 21 - Directory Listing
Modified Thu Jun 28 10:53:55 2012 UTC (4 years, 11 months ago) by anpefi
vignette updated with references

Revision 19 - Directory Listing
Modified Tue Jun 26 08:16:56 2012 UTC (5 years ago) by anpefi
Removal of obsolete and wrong argument 'tag' when calling diffAmova. It caused that build of last revision failed. Checked.

Revision 15 - Directory Listing
Modified Wed Jun 20 15:38:54 2012 UTC (5 years ago) by anpefi
assignation of pops,DM.MSL and DM.NMl into global Environment. This allow for further analysis of distance matrices outside of msap

Revision 14 - Directory Listing
Modified Wed Jun 20 07:44:50 2012 UTC (5 years ago) by anpefi
Added some missing png files to /vignette that caused build fail in R-Forge

Revision 13 - Directory Listing
Modified Tue Jun 19 18:21:59 2012 UTC (5 years ago) by anpefi
A lot of changes and fixes. Added extra arguments to msap(). Added nj tree. R CMD checks OK.

Revision 11 - Directory Listing
Modified Mon Jun 18 10:47:14 2012 UTC (5 years ago) by anpefi
updating documentation

Revision 10 - Directory Listing
Modified Mon Jun 18 10:18:14 2012 UTC (5 years ago) by anpefi
Added removal (by default but optional) of non polymorphic loci

Revision 6 - Directory Listing
Modified Sat Jun 16 11:22:05 2012 UTC (5 years ago) by anpefi
Added some links to the website: vignette, my personal website, changed support. Some other minor changes

Revision 5 - Directory Listing
Modified Sat Jun 16 00:18:45 2012 UTC (5 years ago) by anpefi
Simplification of code in msap.R. Added different files for different functions. Added AFLP mode

Revision 4 - Directory Listing
Modified Fri Jun 15 19:07:01 2012 UTC (5 years ago) by anpefi
Version 0.1-2. Improvments on the webpage. Adding vignette (User manual). Adding NAMESPACE. Clean up and several fixes in order to pass R CMD check. Added new loading of data including locus names. Extending help pages

Revision 2 - Directory Listing
Modified Thu Jun 14 21:04:34 2012 UTC (5 years ago) by anpefi
Intial commit with first basic version 0.1.1

Revision 1 - Directory Listing
Added Thu Sep 15 15:26:09 2011 UTC (5 years, 9 months ago) by stefan7th
small themeroot fix

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