'genet', 'phylog', 'listw' and 'neig' in ade4

genet in ade4

Removed 🚮

• char2genet, count2genet, freq2genet, dist.genet, fuzzygenet

Data

• the datasets hdpg, casitas, apis108 and chevaine which contain genetic data and are no longer consistent in ade4. Must be translocated to adedata. Not currently included in adegenet.

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phylog in ade4

Removed 🚮

• EH, randEH, optimEH, orisaved

Exported

• Graphical functions : plot.phylog (S3 method), table.phylog, dotchart.phylog, symbols.phylog, radial.phylog --> to implement in adegraphics ??
• print.phylog (S3 method), phylog.extract, phylog.permut
• newick2phylog, hclust2phylog, taxo2phylog
• variance.phylog : "Object of class 'phylog' expected"
• enum.phylog : "Object of class 'phylog' expected"
• originality : "Object of class 'phylog' expected"
• as.taxo, dist.taxo : create and manage object of "taxo" class (used in the "taxo2phylog" function)
• gearymoran : Moran's I and Geary'c randomization tests for spatial and phylogenetic autocorrelation
• PI2newick : import data files from the PI Package of Abouheif (1999)
• mld(..., phylog=NULL, ...)

Not exported

• table.prepare(..., pos = "pylog")
• newick2phylog.addtools

newick2phylog is the only one function that creates an object of phylog class.

"phylog objects from ade4 are now deprecated; users are encouraged to use the adephylo package, which uses phylo and phylo4 objects directly.". See in https://www.rdocumentation.org/packages/phylobase/versions/0.6.8/topics/phylog-class

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listw in ade4

Removed 🚮

• multispati, print.multispati, plot.multispati, summary.multispati, multispati.rtest, multispati.randtest

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neig in ade4

Removed 🚮

• orthogram
• the data: elec88$neig, atya$neig, buech$neig, sarcelles$neig, kponds$neig, zealand$neig, tintoodiel$neig, mafragh$neig,

Exported

• neig, nb2neig, neig2nb, neig2mat, dist.neig, scores.neig
• print.neig (S3 method), summary.neig (S3 method)
• orthobasis.neig
• area.plot
• gridrowcol (output), mstree (output)

Non exported

• neig.util.GtoL, neig.util.LtoG

Used in

• s.kde2d, s.label, s.logo, s.value, s.image, dotcircle (example)
• gearymoran (example), multispati (example), multispati.randtest (example)
• the data: avijons (example), westafrica (example), oribatib (example), julliot (example),