Lepi                 package:BSagri                 R Documentation

_I_n_s_e_c_t _c_o_u_n_t_s _o_f _1_2 _S_p_e_c_i_e_s

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

     Simulated data, inpired by a real field investigating the
     potential impact of genetically modified crop on several insect
     species belonging to the same order. The trial was designed as a
     randomized complete block design with 8 blocks (Block), and a
     total of 24 plots. In each block, three treatments (Treatment)
     were randomized: a conventional variety treated with insecticides
     (Ins), a genetically modified variety (GM) without insecticide
     treatment, and the near-isogenic variety (Iso) the to genetically
     modified variety, without insecticide treatment. Individuals were
     counted (after classification to the species level) in two
     different dates in each year of the trial, where the the second
     date was of higher importance for assessment of impacts of GM
     variety on non-target species. In total 12 Species were observed
     during the trial.

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

     data(Lepi)

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

     A data frame with 144 observations on the following 17 variables.

     '_Y_e_a_r' a numeric vector, the year 1, 2, 3

     '_D_a_t_e' a numeric vector, 1 and 2 separating the 2 sampling date in
          each year 

     '_B_l_o_c_k' a numeric vector, with values 1-8, indicator variable for
          the 8 blocks

     '_T_r_e_a_t_m_e_n_t' a factor with three levels identifying the varieties:
          'GM' is the genetically modified variety, 'Ins' the
          conventional variety with insecticide treatment and 'Iso' the
          near isognic line without insecticide treatment

     '_P_l_o_t' a factor with 24 levels, identifying the individual plots

     '_S_p_1' counts of taxon 1

     '_S_p_2' counts of taxon 2

     '_S_p_3' counts of taxon 3

     '_S_p_4' counts of taxon 4

     '_S_p_5' counts of taxon 5

     '_S_p_6' counts of taxon 6

     '_S_p_7' counts of taxon 7

     '_S_p_8' counts of taxon 8

     '_S_p_9' counts of taxon 9

     '_S_p_1_0' counts of taxon 10

     '_S_p_1_1' counts of taxon 11

     '_S_p_1_2' counts of taxon 12

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

     Simulated data.

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

     data(Lepi)

     str(Lepi)

     summary(Lepi)

     SPEC<-names(Lepi)[-(1:5)]

     # Occurrence

     occur<-lapply(X=Lepi[,SPEC], FUN=function(x){length(which(x>0))})

     unlist(occur)

     # Species with reasonable occurence in the whole data:

     SPEC2<-SPEC[c(1,2,3,6,8,9,11)]

     pairs(Lepi[,SPEC2])

     # 

     layout(matrix(1:2, ncol=1 ))
     par(mar=c(2,8,2,1))

     boxplot(Sp2 ~ Treatment*Year, data=Lepi, main="Species 2",
      las=1, horizontal=TRUE, col=c("red","white","white"))

     boxplot(Sp3 ~ Treatment*Year, data=Lepi, main="Species 3",
      las=1, horizontal=TRUE, col=c("red","white","white"))

     layout(matrix(1:3, ncol=1 ))
     par(mar=c(2,8,2,1))

     boxplot(Sp1 ~ Treatment*Year, data=Lepi, main="Species 1",
      las=1, horizontal=TRUE, col=c("red","white","white"))

     boxplot(Sp8 ~ Treatment*Year, data=Lepi, main="Species 8",
      las=1, horizontal=TRUE, col=c("red","white","white"))

     boxplot(Sp9 ~ Treatment*Year, data=Lepi, main="Species 9",
      las=1, horizontal=TRUE, col=c("red","white","white"))

