R-Forge Project: msap - News

All development of msap moved to github

anpefi@users.r-forge.r-project.org (Andrés Pérez-Figueroa) — Thu, 28 Dec 2017 11:33:22 GMT

For some convenience reasons, the development of msap (source code and issue tracker) is now maintained in github: https://github.com/anpefi/msap

Please note that no further updates will be notified in this R-Forge page

Problems with subset?: Update to 1.1.9

anpefi@users.r-forge.r-project.org (Andrés Pérez-Figueroa) — Wed, 07 Jan 2015 11:44:03 GMT

A bug in msap <=1.1.8 has been reported. In some circumstances the program crashes while calculating the pairwisePhiST reporting the following message:

Error in subset.default(DM, c(p1, p2)) : 'subset' must be logical.

This bug has been solved in version 1.1.9, but this version is not available on CRAN yet, so if you are experiencing that bug you should update to msap 1.1.9 from R-Forge repository: install.packages("msap", repos="http://R-Forge.R-project.org")

msap 1.1.8 on CRAN now

anpefi@users.r-forge.r-project.org (Andrés Pérez-Figueroa) — Mon, 12 May 2014 08:35:55 GMT

A new stable version of msap is available now in the CRAN. It solves some possible problems arisen in previous versions so it is highly recommended to update msap to this new version.

The most important changes are:
1. A problem causing crash when NJ or PCoA were performed for more than 7 groups is fixed now.
2. Some package dependencies were removed as they were no needed.
3. The way to obtain the distance matrices was simplified and tuned. This yields quantitatively different values in the coordinates of PCoA, although the eigenvalues and the relative patterns remain the same. Slightly different values on the AMOVAS could also happen.
4. A binary for Windows built in the last major release of R is now availiable.

The paper describing msap in Molecular Ecology Resources

anpefi@users.r-forge.r-project.org (Andrés Pérez-Figueroa) — Fri, 08 Feb 2013 19:02:59 GMT

The paper, describing msap and its utility, for Molecular Ecology Resources is available as online early view at http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12064/abstract.

So, if you use msap I would be very grateful if you include the following citation:
Pérez-Figueroa, A. (2013), msap: a tool for the statistical analysis of methylation-sensitive amplified polymorphism data. Molecular Ecology Resources. doi: 10.1111/1755-0998.12064

version 1.1.2 on CRAN now

anpefi@users.r-forge.r-project.org (Andrés Pérez-Figueroa) — Fri, 08 Feb 2013 09:18:34 GMT

It has been published a new update on the CRAN. Now it is possible to get distance matrices and transformed data for MSL and NML as a returning list from the msap function. This is useful for those interested in further self-made analysis within R.

Very important update: new version fixing a bug

anpefi@users.r-forge.r-project.org (Andrés Pérez-Figueroa) — Wed, 06 Feb 2013 19:30:51 GMT

A new revision (31) has been committed and it would build the version 1.1.1 of msap. This is a VERY IMPORTANT UPDATE as it fixes a bug present in previous versions that could slightly affect the result of any analysis made with msap. In the manual is stated that polymorphic loci were those with at least two occurrences of both states (methylayted and unmethylated), but there was an error in the code that consider as polymorphic those with more than two occurrences of both states. This could be a relevant bug making that, in some datasets, msap underestimated the number of polymorphic loci.
Please ensure do not use any previous version (<1.1.1) for a safe analysis. This new version would be availiable from the repositories in the next hours.

I apologize for any inconvenient caused by this bug that escaped from my tests.

Andrés.

msap 1.1.0 released

anpefi@users.r-forge.r-project.org (Andrés Pérez-Figueroa) — Wed, 14 Nov 2012 23:57:42 GMT

A new version of msap has been released at CRAN. As major new feature, now the fragment classification is done for each primer combination independently (allowing for different error rates for each). Furthermore, the 'uninformative' parameters has been changed by 'no.bands' (see manual for details).

New version: msap 1.0.2

anpefi@users.r-forge.r-project.org (Andrés Pérez-Figueroa) — Thu, 04 Oct 2012 19:54:05 GMT

There is a new version available in the Daily repository (soon also in CRAN). This version (1.0.2) fixes a bug causing crash of the program when dealing with datasets without NML.

version 1.0

anpefi@users.r-forge.r-project.org (Andrés Pérez-Figueroa) — Tue, 11 Sep 2012 13:16:30 GMT

msap 1.0 is available at the CRAN. This is the first full stable version with all analyses that could be considered as a 'minimum'. Further versions with some additions will be coming soon.

version 1.0 in cran

anpefi@users.r-forge.r-project.org (Andrés Pérez-Figueroa) — Tue, 11 Sep 2012 13:12:42 GMT

msap 1.0 is available at the CRAN. This is the first full stable version with all analyses that could be considered as a 'minimum'. Further versions with some additions will be coming soon.