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72 divc divc Rao’s diversity coefficient also called quadratic entropy Description Calculates Rao’s diversity coefficient within samples. Usage divc(df, dis, scale) Arguments df dis scale a data frame with elements as rows, samples as columns, and abundance, presenceabsence or frequencies as entries an object of class dist containing distances or dissimilarities among elements. If dis is NULL, Gini-Simpson index is performed. a logical value indicating whether or not the diversity coefficient should be scaled by its maximal value over all frequency distributions. Value Returns a data frame with samples as rows and the diversity coefficient within samples as columns Author(s) Sandrine Pavoine 〈pavoine@biomserv.univ-lyon1.fr〉 References Rao, C.R. (1982) Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology, 21, 24–43. Gini, C. (1912) Variabilitá e mutabilitá. Universite di Cagliari III, Parte II. Simpson, E.H. (1949) Measurement of diversity. Nature, 163, 688. Champely, S. and Chessel, D. (2002) Measuring biological diversity using Euclidean metrics. Environmental and Ecological Statistics, 9, 167–177. Examples data(ecomor) dtaxo
divcmax 73 divcmax Maximal value of Rao’s diversity coefficient also called quadratic entropy Description Usage For a given dissimilarity matrix, this function calculates the maximal value of Rao’s diversity coefficient over all frequency distribution. It uses an optimization technique based on Rosen’s projection gradient algorithm and is verified using the Kuhn-Tucker conditions. divcmax(dis, epsilon, comment) Arguments dis epsilon comment an object of class dist containing distances or dissimilarities among elements. a tolerance threshold : a frequency is non null if it is higher than epsilon. a logical value indicating whether or not comments on the optimization technique should be printed. Value Returns a list value vectors the maximal value of Rao’s diversity coefficient. a data frame containing four frequency distributions : sim is a simple distribution which is equal to D1 1 t D1 , pro is equal to z 1 t z1 , where z is the nonnegative eigenvector of the matrix containing the squared dissimilarities among the elements, met is equal to z 2 , num is a frequency vector maximizing Rao’s diversity coefficient. Author(s) Stéphane Champely 〈Stephane.Champely@univ-lyon1.fr〉 Sandrine Pavoine 〈pavoine@biomserv.univ-lyon1.fr〉 References Rao, C.R. (1982) Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology, 21, 24–43. Gini, C. (1912) Variabilitá e mutabilitá. Universite di Cagliari III, Parte II. Simpson, E.H. (1949) Measurement of diversity. Nature, 163, 688. Champely, S. and Chessel, D. (2002) Measuring biological diversity using Euclidean metrics. Environmental and Ecological Statistics, 9, 167–177. Pavoine, S., Ollier, S. and Pontier, D. (2005) Measuring diversity from dissimilarities with Rao’s quadratic entropy: are any dissimilarities suitable? Theoretical Population Biology, 67, 231–239.
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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
Page 21 and 22: area.plot 21 Value possub cpoint la
Page 23 and 24: arrival 23 # 4 fr.poly
Page 25 and 26: atlas 25 par(mfrow = c(1,1)) all(di
Page 27 and 28: avijons 27 Examples ## Not run: dat
Page 29 and 30: avimedi 29 par(mfcol=c(3,2)) s.valu
Page 31 and 32: acteria 31 Details aviurba$mil cont
Page 33 and 34: aran95 33 eparlog : "Savings and lo
Page 35 and 36: etween 35 par(mfrow = c(1,1)) betwe
Page 37 and 38: icenter.wt 37 Format Source A list
Page 39 and 40: setal97 39 Format bsetal97 is a lis
Page 41 and 42: utterfly 41 Examples data(buech) pa
Page 43 and 44: capitales 43 is.euclid(d1) # TRUE p
Page 45 and 46: carniherbi49 45 Format Source carni
Page 47 and 48: cca 47 Usage data(casitas) Format T
Page 49 and 50: chatcat 49 s.match(iv1$ls, iv1$li,
Page 51 and 52: chazeb 51 chazeb Charolais-Zebus De
Page 53 and 54: cnc2003 53 Usage data(clementines)
Page 55 and 56: coinertia 55 coinertia Coinertia An
Page 57 and 58: coleo 57 coleo Table of Fuzzy Biolo
Page 59 and 60: corvus 59 Examples data(friday87) f
Page 61 and 62: disc 61 disc Rao’s dissimilarity
Page 63 and 64: discrimin.coa 63 See Also lda in pa
Page 65 and 66: dist.dudi 65 5 = Czekanowski (1913)
Page 67 and 68: dist.genet 67 Let P the table of ge
Page 69 and 70: dist.prop 69 Value returns a distan
Page 71: dist.quant 71 Arguments df method d
Page 75 and 76: dotchart.phylog 75 Usage dotchart.p
Page 77 and 78: doubs 77 doubs Pair of Ecological T
Page 79 and 80: dpcoa 79 Value option csize the fun
Page 81 and 82: dudi.acm 81 Value as.dudi and all t
Page 83 and 84: dudi.coa 83 Examples data(ours) sum
Page 85 and 86: dudi.fca 85 Arguments df eff scannf
Page 87 and 88: dudi.hillsmith 87 data(bsetal97) w
Page 89 and 90: dudi.mix 89 Details If df contains
Page 91 and 92: dudi.pca 91 dudi.pca Principal Comp
Page 93 and 94: dudi.pco 93 Usage dudi.pco(d, row.w
Page 95 and 96: ecg 95 ecg Electrocardiogram data D
Page 97 and 98: elec88 97 References See a data des
Page 99 and 100: escopage 99 escopage K-tables of wi
Page 101 and 102: foucart 101 References Cheverud, J.
Page 103 and 104: friday87 103 friday87 Faunistic K-t
Page 105 and 106: fuzzygenet 105 fuzzygenet Reading a
Page 107 and 108: genet 107 Value Returns an object o
Page 109 and 110: genet 109 Value char2genet returns
Page 111 and 112: granulo 111 Examples if(require(pix
Page 113 and 114: hdpg 113 Examples w
Page 115 and 116: humDNAm 115 Usage data(housetasks)
Page 117 and 118: inertia.dudi 117 inertia.dudi Stati
Page 119 and 120: is.euclid 119 contour is a data fra
Page 121 and 122: 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.,
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mantel.randtest 149 Source Belair,
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maples 151 Arguments m1 m2 nrepet a
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mcoa 153 Source Codes for rows and
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meau 155 Examples data(friday87) w1
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mfa 157 mfa Multiple Factorial Anal
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microsatt 159 Format microsatt is a
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mld 161 Examples data(mjrochet) mjr
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monde84 163 Format Source mollusc i
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mstree 165 mstree Minimal Spanning
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multispati 167 Value Returns an obj
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multispati.randtest 169 w1.msm
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neig 171 Author(s) Daniel Chessel S
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neig 173 #hist(dist, nclass = 50) m
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newick2phylog 175 References Bauwen
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niche 177 w[19]
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njplot 179 Author(s) Daniel Chessel
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optimEH 181 Source Example 357 in:
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originality 183 Details Variables o
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orisaved 185 orisaved Maximal or mi
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orthobasis 187 Value All the functi
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orthogram 189 orthogram Orthonormal
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ours 191 Examples # a phylogenetic
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palm 193 palm Phylogenetic and quan
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pcaiv 195 pcaiv Principal component
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pcaivortho 197 Arguments dudi df sc
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perthi02 199 Author(s) Daniel Chess
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phylog 201 paths droot call Wmat Wd
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plot.phylog 203 f.phylog circle cle
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presid2002 205 ## Not run: # plot a
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procuste 207 Format procella is a l
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procuste.randtest 209 References Di
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pta 211 Arguments df1 df2 nrepet a
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quasieuclid 213 Author(s) Pierre Ba
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andtest-internal 215 References Nee
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andtest.amova 217 Examples par(mfro
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andtest.coinertia 219 randtest.coin
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ankrock 221 # Df Pillai approx F nu
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hone 223 rhone Physico-Chemistry Da
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lq 225 nf RV eig lw cw tab li l1 co
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test 227 Examples ## Not run: data(
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test.discrimin 229 References Romes
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s.chull 231 addaxes cgrid sub csub
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s.class 233 Examples xy 0) coul 0
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s.corcircle 235 possub = "bottomrig
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s.distri 237 Value clabel cpoint pc
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s.image 239 Examples data(rpjdl) co
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s.kde2d 241 s.image(t3012$xy, scale
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s.label 243 Arguments Value dfxy xa
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s.logo 245 Value xax yax neig cneig
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s.multinom 247 Value cgrid a charac
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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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