xorder                 package:mefa                 R Documentation

_M_a_k_e_s _O_b_j_e_c_t _o_f _C_l_a_s_s '_x_o_r_d_e_r'

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

     The function makes an object of class 'xorder' from an attribute
     table (data frame) based on comparison with an 'xcount' object.
     Data frame subsetting is made according to results of function
     'check.attrib'.

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

     xorder(xc, which = c("samples", "species"), attrib, index = 1)

_A_r_g_u_m_e_n_t_s:

      xc: an object of class 'xcount'.

   which: switch for rows ('"samples"') or columns ('"species"') of the
          'xcount' object to be compared according to 'index'.

  attrib: data frame to be checked.

   index: column identifier within 'attrib' to be compared according to
          row/column names (as sample/species identifiers) of the
          'xcount' object according to value of 'which'.  By default it
          is the first column of data frame 'attrib'.

_V_a_l_u_e:

     A result is an object of class 'xorder'. 

   which: the value of the 'which' argument, either '"samples"' or
          '"species"'.

check.setrel: 'set.relation' value of function 'check.attrib'.

check.dupl: 'duplicate' value of function 'check.attrib'.

    data: data frame, ordered and subsetted according to the 'xcount'
          object.

_A_u_t_h_o_r(_s):

     Peter Solymos, Solymos.Peter@aotk.szie.hu, <URL:
     http://www.univet.hu/users/psolymos/personal/>

_S_e_e _A_l_s_o:

     'check.attrib', 'mefa', 'xcount'

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

     ### Example 1: simple atrificial data

     ss <- data.frame(
     cbind(
     c("sample1","sample1","sample2","sample2","sample3","sample4"),
     c("species1","species1","species1","species2","species3","zero.count"),
     c("male","female","male","female","male","male")
     ),
     c(1, 2, 10, 3, 4, 1)
     )
     colnames(ss) <- c("sample.id", "species.id", "gender", "catch")

     spectab <- as.data.frame(rbind(
             c("species3", "family1", "1"),
             c("species2", "family2", "5"),
             c("species1", "family1", "2"),
             c("species5", "family2", "1"),
             c("species4", "family1", "10")
     ))
     colnames(spectab) <- c("species", "taxonomy", "size")

     sampletab <- as.data.frame(rbind(
             c("sample3", "bad"),
             c("sample1", "good"),
             c("sample2", "good"),
             c("sample4", "bad")))
     colnames(sampletab) <- c("sample", "quality")

     xct <- xcount(sscount(ss, "zero.count"))

     xo1 <- xorder(xct, "samples", sampletab, 1)
     xo2 <- xorder(xct, "species", spectab, 1)

     ### Example 2: field data of Villany Hills

     ## Not run: 
     data(vtable, vsample, landsnail)

     vt <- as.xcount(vtable, FALSE)

     spec <- xorder(vt, which="species", landsnail, 2)
     spec

     sampl <- xorder(vt, which="samples", vsample)
     sampl
     ## End(Not run)

