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200 phylog Examples data(perthi02) plot(discrimin.coa(perthi02$tab, perthi02$cla, scan = FALSE)) phylog Phylogeny Description Create and use objects of class phylog. phylog.extract returns objects of class phylog. It extracts sub-trees from a tree. phylog.permut returns objects of class phylog. It creates the different representations compatible with tree topology. Usage ## S3 method for class 'phylog': print(x, ...) phylog.extract(phylog, node, distance = TRUE) phylog.permut(phylog, list.nodes = NULL, distance = TRUE) Arguments Value x, phylog : an object of class phylog ... : further arguments passed to or from other methods node distance list.nodes Returns a list of class phylog : : a string of characters giving a node name. <strong>The</strong> functions extracts the tree rooted at this node. : if TRUE, both functions retain branch lengths. If FALSE, they returns tree with arbitrary branch lengths (each branch length equals one) : a list which elements are vectors of string of character corresponding to direct descendants of nodes. This list defines one representation compatible with tree topology among the set of possibilities. tre leaves nodes parts : a character string of the phylogenetic tree in Newick format whithout branch length values : a vector which names corresponds to leaves and values gives the distance between leaves and nodes closest to these leaves : a vector which names corresponds to nodes and values gives the distance between nodes and nodes closest to these leaves : a list which elements gives the direct descendants of each nodes
phylog 201 paths droot call Wmat Wdist Wvalues Wscores Amat Avalues Adim Ascores Aparam Bindica Bscores Bvalues Blabels : a list which elements gives the path leading from the root to taxonomic units (leaves and nodes) : a vector which names corresponds to taxonomic units and values gives distance between taxonomic units and the root : call : a phylogenetic link matrix, generally called the covariance matrix. Matrix values W mat ij correspond to path length that lead from root to the first common ancestor of the two leaves i and j : a phylogenetic distance matrix of class ’dist’. Matrix values W dist ij correspond to √ d ij where d ij is the classical distance between two leaves i and j : a vector with the eigen values of Wmat : a data frame with eigen vectors of Wmat. This data frame defines an orthobasis that could be used to calculate the orthonormal decomposition of a biological trait on a tree. : a phylogenetic link matrix stemed from Abouheif’s test and defined in Ollier et al. (submited) : a vector with the eigen values of Amat : number of positive eigen values : a data frame with eigen vectors of Amat. This data frame defines an orthobasis that could be used to calculate the orthonormal decomposition of a biological trait on a tree. : a data frame with attributes associated to nodes. : a data frame giving for some taxonomic units the partition of leaves that is associated to its : a data frame giving an orthobasis defined by Ollier et al. (submited) that could be used to calculate the orthonormal decomposition of a biological trait on a tree. : a vector giving the degree of phylogenetic autocorrelation for each vectors of Bscores (Moran’s form calculated with the matrix Wmat) : a vector giving for each nodes the name of the vector of Bscores that is associated to its Author(s) Daniel Chessel Sébastien Ollier 〈ollier@biomserv.univ-lyon1.fr〉 References Ollier, S., Couteron, P. and Chessel, D. (2005) Orthonormal transforms to detect and describe phylogenetic autocorrelation. Biometrics (in press).
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The ade4 Package February 16, 2008
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R topics documented: 3 dudi.acm . .
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R topics documented: 5 plot.phylog
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EH 7 EH Amount of Evolutionary Hist
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RV.rtest 9 RV.rtest Monte-Carlo Tes
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acacia 11 Format abouheif.eg is a l
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add.scatter 13 Usage add.scatter(fu
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ade4toR 15 Arguments fictab ficcoln
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amova 17 amova Analysis of molecula
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ardeche 19 ardeche Fauna Table with
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area.plot 21 Value possub cpoint la
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arrival 23 # 4 fr.poly
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atlas 25 par(mfrow = c(1,1)) all(di
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avijons 27 Examples ## Not run: dat
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avimedi 29 par(mfcol=c(3,2)) s.valu
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acteria 31 Details aviurba$mil cont
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aran95 33 eparlog : "Savings and lo
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etween 35 par(mfrow = c(1,1)) betwe
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icenter.wt 37 Format Source A list
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setal97 39 Format bsetal97 is a lis
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utterfly 41 Examples data(buech) pa
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capitales 43 is.euclid(d1) # TRUE p
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carniherbi49 45 Format Source carni
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cca 47 Usage data(casitas) Format T
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chatcat 49 s.match(iv1$ls, iv1$li,
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chazeb 51 chazeb Charolais-Zebus De
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cnc2003 53 Usage data(clementines)
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coinertia 55 coinertia Coinertia An
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coleo 57 coleo Table of Fuzzy Biolo
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corvus 59 Examples data(friday87) f
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disc 61 disc Rao’s dissimilarity
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discrimin.coa 63 See Also lda in pa
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dist.dudi 65 5 = Czekanowski (1913)
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dist.genet 67 Let P the table of ge
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dist.prop 69 Value returns a distan
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dist.quant 71 Arguments df method d
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divcmax 73 divcmax Maximal value of
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dotchart.phylog 75 Usage dotchart.p
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doubs 77 doubs Pair of Ecological T
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dpcoa 79 Value option csize the fun
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dudi.acm 81 Value as.dudi and all t
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dudi.coa 83 Examples data(ours) sum
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dudi.fca 85 Arguments df eff scannf
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dudi.hillsmith 87 data(bsetal97) w
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dudi.mix 89 Details If df contains
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dudi.pca 91 dudi.pca Principal Comp
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dudi.pco 93 Usage dudi.pco(d, row.w
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ecg 95 ecg Electrocardiogram data D
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elec88 97 References See a data des
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escopage 99 escopage K-tables of wi
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foucart 101 References Cheverud, J.
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friday87 103 friday87 Faunistic K-t
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fuzzygenet 105 fuzzygenet Reading a
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genet 107 Value Returns an object o
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genet 109 Value char2genet returns
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granulo 111 Examples if(require(pix
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hdpg 113 Examples w
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humDNAm 115 Usage data(housetasks)
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inertia.dudi 117 inertia.dudi Stati
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is.euclid 119 contour is a data fra
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julliot 121 Format julliot is a lis
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kcponds 123 Examples data(jv73) s.l
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kdist 125 Details The attributs of
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kdisteuclid 127 Value returns a lis
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kplot 129 kplot Generic Function fo
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kplot.mfa 131 csub possub a charact
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kplot.sepan 133 which.graph an opti
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kplot.statis 135 w
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ktab 137 Value plot.krandtest draws
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ktab.data.frame 139 Examples data(f
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ktab.list.dudi 141 Examples data(jv
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ktab.within 143 Examples data(meau)
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lingoes 145 Examples data(lascaux)
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macaca 147 References Bauwens, D.,
Page 149 and 150: mantel.randtest 149 Source Belair,
Page 151 and 152: maples 151 Arguments m1 m2 nrepet a
Page 153 and 154: mcoa 153 Source Codes for rows and
Page 155 and 156: meau 155 Examples data(friday87) w1
Page 157 and 158: mfa 157 mfa Multiple Factorial Anal
Page 159 and 160: microsatt 159 Format microsatt is a
Page 161 and 162: mld 161 Examples data(mjrochet) mjr
Page 163 and 164: monde84 163 Format Source mollusc i
Page 165 and 166: mstree 165 mstree Minimal Spanning
Page 167 and 168: multispati 167 Value Returns an obj
Page 169 and 170: multispati.randtest 169 w1.msm
Page 171 and 172: neig 171 Author(s) Daniel Chessel S
Page 173 and 174: neig 173 #hist(dist, nclass = 50) m
Page 175 and 176: newick2phylog 175 References Bauwen
Page 177 and 178: niche 177 w[19]
Page 179 and 180: njplot 179 Author(s) Daniel Chessel
Page 181 and 182: optimEH 181 Source Example 357 in:
Page 183 and 184: originality 183 Details Variables o
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Page 187 and 188: orthobasis 187 Value All the functi
Page 189 and 190: orthogram 189 orthogram Orthonormal
Page 191 and 192: ours 191 Examples # a phylogenetic
Page 193 and 194: palm 193 palm Phylogenetic and quan
Page 195 and 196: pcaiv 195 pcaiv Principal component
Page 197 and 198: pcaivortho 197 Arguments dudi df sc
Page 199: perthi02 199 Author(s) Daniel Chess
Page 203 and 204: plot.phylog 203 f.phylog circle cle
Page 205 and 206: presid2002 205 ## Not run: # plot a
Page 207 and 208: procuste 207 Format procella is a l
Page 209 and 210: procuste.randtest 209 References Di
Page 211 and 212: pta 211 Arguments df1 df2 nrepet a
Page 213 and 214: quasieuclid 213 Author(s) Pierre Ba
Page 215 and 216: andtest-internal 215 References Nee
Page 217 and 218: andtest.amova 217 Examples par(mfro
Page 219 and 220: andtest.coinertia 219 randtest.coin
Page 221 and 222: ankrock 221 # Df Pillai approx F nu
Page 223 and 224: hone 223 rhone Physico-Chemistry Da
Page 225 and 226: lq 225 nf RV eig lw cw tab li l1 co
Page 227 and 228: test 227 Examples ## Not run: data(
Page 229 and 230: test.discrimin 229 References Romes
Page 231 and 232: s.chull 231 addaxes cgrid sub csub
Page 233 and 234: s.class 233 Examples xy 0) coul 0
Page 235 and 236: s.corcircle 235 possub = "bottomrig
Page 237 and 238: s.distri 237 Value clabel cpoint pc
Page 239 and 240: s.image 239 Examples data(rpjdl) co
Page 241 and 242: s.kde2d 241 s.image(t3012$xy, scale
Page 243 and 244: s.label 243 Arguments Value dfxy xa
Page 245 and 246: s.logo 245 Value xax yax neig cneig
Page 247 and 248: s.multinom 247 Value cgrid a charac
Page 249 and 250: s.traject 249 Value Returns in a hi
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s.value 251 Examples rw
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santacatalina 253 par(mfrow = c(3,4
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scalewt 255 scalewt Centring and Sc
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scatter 257 Author(s) See Also Dani
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scatter.dudi 259 Arguments x xax ya
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scatter.fca 261 scatter.fca Plot of
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sco.distri 263 banque.acm
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score 265 Arguments score df fac cl
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score.coa 267 Arguments x xax which
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score.mix 269 par(mfrow = c(1,1)) s
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seconde 271 seconde Students and Su
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skulls 273 skulls Morphometric Evol
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steppe 275 C.T4 TL TC T4 a data fra
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suprow 277 Details If supcol.defaul
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symbols.phylog 279 symbols.phylog R
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table.cont 281 Format Source t3012
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table.paint 283 Usage table.dist(d,
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table.value 285 labels.col clabel.c
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tarentaise 287 Format tarentaise is
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testdim 289 testdim Function to per
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tithonia 291 s.label(tintoodiel$xy,
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toxicity 293 points(ref,xyz[,2], pc
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triangle.plot 295 show.position a l
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trichometeo 297 Examples data (euro
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uniquewt.df 299 Source Data were ob
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vegtf 301 Value Returns a list cont
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westafrica 303 Details The columns
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within 305 afri.ms
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withinpca 307 withinpca Normed with
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worksurv 309 References Cazes, P.,
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zealand 311 Examples data(yanomama)
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Index ∗Topic array cailliez, 36 d
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INDEX 315 krandtest, 130 randtest,
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INDEX 317 bf88, 30 bicenter.wt, 31
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INDEX 319 plot.procuste (procuste),
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INDEX 321 wavelet.filter, 181 westa
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