ecomor                 package:ade4                 R Documentation

_E_c_o_m_o_r_p_h_o_l_o_g_i_c_a_l _C_o_n_v_e_r_g_e_n_c_e

_D_e_s_c_r_i_p_t_i_o_n:

     This data set gives ecomorphological informations about 129 bird
     species.

_U_s_a_g_e:

     data(ecomor)

_F_o_r_m_a_t:

     'ecomor' is a list of 7 components.

     _f_o_r_s_u_b is a data frame with 129 species, 6 variables (the feeding
          place classes):  foliage, ground , twig , bush, trunk and
          aerial feeders. These dummy variables indicate the use (1) 
          or  no use (0) of a given feeding place by a species. 

     _d_i_e_t is a data frame with 129 species and 8 variables (diet
          types): Gr (granivorous: seeds),  Fr (frugivorous: berries,
          acorns, drupes), Ne (frugivorous: nectar), Fo (folivorous:
          leaves),  In (invertebrate feeder: insects, spiders,
          myriapods, isopods, snails, worms),  Ca (carnivorous: flesh
          of small vertebrates), Li (limnivorous: invertebrates in
          fresh water), and Ch (carrion feeder). These dummy variables
          indicate the use (1)  or  no use (0) of a given diet type by
          a species.

     _h_a_b_i_t_a_t is a data frame with 129 species, 16 dummy variables (the
          habitats).  These variables indicate the species presence (1)
          or the species absence (0) in a given habitat.

     _m_o_r_p_h_o is a data frame with 129 species abd 8 morphological
          variables: wingl (Wing length, mm),  taill (Tail length, mm),
          culml (Culmen length, mm), bilh (Bill height, mm), bilw (Bill
          width, mm),  tarsl (Tarsus length, mm), midtl (Middle toe
          length, mm) and weig (Weight, g).

     _t_a_x_o is a data frame with 129 species and 3 factors: Genus, Family
          and Order. It is a data frame of class ''taxo'': the
          variables are factors giving nested classifications.

     _l_a_b_e_l_s is a data frame with vectors of the names of species
          (complete and in abbreviated form.

     _c_a_t_e_g is a data frame with 129 species, 2 factors : 'forsub'
          summarizing the feeding place and  'diet' the diet type.

_S_o_u_r_c_e:

     Blondel, J., Vuilleumier, F., Marcus, L.F., and Terouanne, E.
     (1984). Is there ecomorphological convergence  among mediterranean
     bird communities of Chile, California, and France. In
     _Evolutionary Biology_  (eds M.K. Hecht, B. Wallace and R.J.
     MacIntyre), 141-213, *18*. Plenum Press, New York.

_E_x_a_m_p_l_e_s:

     data(ecomor)
     ric <- apply(ecomor$habitat, 2, sum)
     s.corcircle(dudi.pca(log(ecomor$morpho), scan = FALSE)$co)

     forsub <- data.frame(t(apply(ecomor$forsub, 1,
          function (x) x/sum(x))))
     pca1 <- dudi.pca(forsub, scan = FALSE, scale = FALSE)
     s.arrow(pca1$c1)
     w <- as.matrix(forsub)
     s.label(w, clab = 0, add.p = TRUE, cpoi = 2)

     diet <- data.frame(t(apply(ecomor$diet, 1,
          function (x) x/sum(x))))
     pca2 <- dudi.pca(diet, scan = FALSE, scale = FALSE)
     s.arrow(pca2$c1)
     w <- as.matrix(diet)
     s.label(w, clab = 0, add.p = TRUE, cpoi = 2)
     ## Not run: 
     dmorpho <- dist.quant(log(ecomor$morpho), 3)
     dhabitat <- dist.binary(ecomor$habitat, 1)

     mantel.randtest(dmorpho, dhabitat)
     RV.rtest(pcoscaled(dmorpho), pcoscaled(dhabitat), 999)
     procuste.randtest(pcoscaled(dmorpho), pcoscaled(dhabitat))

     ecophy <- taxo2phylog(ecomor$taxo)
     table.phylog(ecomor$habitat, ecophy, clabel.n = 0.5, f = 0.6,
          clabel.c = 0.75, clabel.r = 0.5, csi = 0.75, cleg = 0)
     plot.phylog(ecophy, clabel.n = 0.75, clabel.l = 0.75,
          labels.l = ecomor$labels[,"latin"])
     dtaxo <- ecophy$Wdist
     mantel.randtest(dmorpho, dtaxo)
     mantel.randtest(dhabitat, dtaxo)
     ## End(Not run)

