plantTraits         package:cluster         R Documentation(latin1)

_P_l_a_n_t _S_p_e_c_i_e_s _T_r_a_i_t_s _D_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     This dataset constitutes a description of 136 plant species
     according to biological attributes (morphological or reproductive)

_U_s_a_g_e:

     data(plantTraits)

_F_o_r_m_a_t:

     A data frame with 136 observations on the following 31 variables.

     '_p_d_i_a_s' Diaspore mass (mg)

     '_l_o_n_g_i_n_d_e_x' Seed bank longevity

     '_d_u_r_f_l_o_w' Flowering duration

     '_h_e_i_g_h_t' Plant height, an ordered factor with levels '1' < '2' <
          ... < '8'.

     '_b_e_g_f_l_o_w' Time of first flowering, an ordered factor with levels
          '1' < '2' < '3' < '4' < '5' < '6' < '7' < '8' < '9'

     '_m_y_c_o_r' Mycorrhizas, an ordered factor with levels '0'never < '1'
          sometimes< '2'always

     '_v_e_g_a_e_r' aerial vegetative propagation, an ordered factor with
          levels '0'never < '1' present but limited< '2'important.

     '_v_e_g_s_o_u_t' underground vegetative propagation, an ordered factor
          with 3 levels identical to 'vegaer' above.

     '_a_u_t_o_p_o_l_l' selfing pollination, an ordered factor with levels
          '0'never < '1'rare < '2' often< the rule'3'

     '_i_n_s_e_c_t_s' insect pollination, an ordered factor with 5 levels '0'
          < ... < '4'.

     '_w_i_n_d' wind pollination, an ordered factor with 5 levels '0' < ...
          < '4'.

     '_l_i_g_n' a binary factor with levels '0:1', indicating if plant is
          woody.

     '_p_i_q' a binary factor indicating if plant is thorny.

     '_r_o_s' a binary factor indicating if plant is rosette.

     '_s_e_m_i_r_o_s' semi-rosette plant, a binary factor ('0': no; '1': yes).

     '_l_e_a_f_y' leafy plant, a binary factor.

     '_s_u_m_a_n' summer annual, a binary factor.

     '_w_i_n_a_n' winter annual, a binary factor.

     '_m_o_n_o_c_a_r_p' monocarpic perennial, a binary factor.

     '_p_o_l_y_c_a_r_p' polycarpic perennial, a binary factor.

     '_s_e_a_s_a_e_s' seasonal aestival leaves, a binary factor.

     '_s_e_a_s_h_i_v' seasonal hibernal leaves, a binary factor.

     '_s_e_a_s_v_e_r' seasonal vernal leaves, a binary factor.

     '_e_v_e_r_a_l_w' leaves always evergreen, a binary factor.

     '_e_v_e_r_p_a_r_t_i' leaves partially evergreen, a binary factor.

     '_e_l_a_i_o' fruits with an elaiosome (dispersed by ants), a binary
          factor.

     '_e_n_d_o_z_o_o' endozoochorous fruits, a binary factor.

     '_e_p_i_z_o_o' epizoochorous fruits, a binary factor.

     '_a_q_u_a_t' aquatic dispersal fruits, a binary factor.

     '_w_i_n_d_g_l' wind dispersed fruits,  a binary factor.

     '_u_n_s_p' unspecialized mechanism of seed dispersal, a binary factor.

_D_e_t_a_i_l_s:

     Most of factor attributes are not disjunctive. For example, a
     plant can be usually pollinated by insects but sometimes
     self-pollination can occured.

_S_o_u_r_c_e:

     Vallet, Jeanne (2005) _Structuration de communautés végétales et
     analyse comparative de traits biologiques le long d'un gradient
     d'urbanisation_. Mémoire de Master 2
     'Ecologie-Biodiversité-Evolution'; Université Paris Sud XI, 30p.+
     annexes (in french)

_E_x_a_m_p_l_e_s:

     data(plantTraits)

     ## Calculation of a dissimilarity matrix
     library(cluster)
     dai.b <- daisy(plantTraits,
                    type = list(ordratio = 4:11, symm = 12:13, asymm = 14:31))

     ## Hierarchical classification
     agn.trts <- agnes(dai.b, method="ward")
     plot(agn.trts, which.plots = 2, cex= 0.6)
     plot(agn.trts, which.plots = 1)
     cutree6 <- cutree(agn.trts, k=6)
     cutree6

     ## Principal Coordinate Analysis
     cmdsdai.b <- cmdscale(dai.b, k=6)
     plot(cmdsdai.b[, 1:2], asp = 1, col = cutree6)