package mvtnorm is obsolete
On 18 Nov 2011, at 12:22, Jombart, Thibaut wrote:
Dear Federico, mvtnorm is not obsolete, genetics is, and has been so for at least a year I think. The R-genetics project on Bioconductor is meant to replace it.
genetics is still on CRAN btw
I think most functionalities of 'genetics' are available in the packages pegas and adegenet.
Neither have the function genotype() and the corollary function as.genotype(), which are quite useful caculating HWE using other packages -- see hwe.hardy() in package gap. bw F
Cheers Thibaut.
________________________________________ From: r-sig-genetics-bounces at r-project.org [r-sig-genetics-bounces at r-project.org] on behalf of Federico Calboli [f.calboli at imperial.ac.uk] Sent: 18 November 2011 11:43 To: r-sig-genetics at r-project.org Subject: [R-sig-genetics] package mvtnorm is obsolete library(genetics) Loading required package: combinat Attaching package: ?combinat? The following object(s) are masked from ?package:utils?: combn Loading required package: gdata gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. Attaching package: ?gdata? The following object(s) are masked from ?package:Hmisc?: combine The following object(s) are masked from ?package:stats?: nobs The following object(s) are masked from ?package:utils?: object.size Loading required package: gtools Loading required package: mvtnorm NOTE: THIS PACKAGE IS NOW OBSOLETE. The R-Genetics project has developed an set of enhanced genetics packages to replace 'genetics'. Please visit the project homepage at http://rgenetics.org for informtion. Attaching package: ?genetics? Ok, I went on to http://rgenetics.org/trac/rgalaxy but no clear guidance is present on mvtnorm. Aside from the message, wich I am happy to ignore, is there any other thing to do/be aware of? bw F -- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com _______________________________________________ R-sig-genetics mailing list R-sig-genetics at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
-- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com