Plot community assembly index

Plot community assembly index and confidence intervals using a list of index. S3 method for class listofindex.

Usage

# S3 method for class 'listofindex'
plot(x, type = "normal", 
  col.index = c("red", "purple", "olivedrab3"), add.conf = TRUE, 
  color.cond = TRUE, val.quant = c(0.025, 0.975), 
  grid.v = TRUE, grid.h = TRUE, xlim = NULL, ylim = NULL, 
  cex.text = 0.8, plot.ask = FALSE, srt.text = 90, alpha = 0.4, ...)

Arguments

x: A list of index and related null models obtained from to the as.listofindex function.
type: Type of plot. Possible type = "simple", "simple_range", "normal", "barplot" and "bytraits".
col.index: Vector of colors for index.
add.conf: Logical value; Add confidence intervals or not.
color.cond: Logical value; If color.cond = TRUE, color points indicate T-statistics values significatively different from the null model and grey points are not different from null model.
val.quant: Numeric vectors of length 2, giving the quantile to calculate confidence interval. By default val.quant = c(0.025,0.975) for a bilateral test with alpha = 5%.
grid.v: Logical value; print vertical grid or not
grid.h: Logical value; print horizontal grid or not
xlim: Numeric vectors of length 2, giving the x coordinates range
ylim: Numeric vectors of length 2, giving the y coordinates range
cex.text: Numeric value; the magnification to be used for text relative to the current setting of cex
plot.ask: Logical value; ask for plotting the next plot or not.
srt.text: Degree of rotation for text.
alpha: Degree of transparency for null models aera.
...: Any additional arguments are passed to the plot function creating the core of the plot and can be used to adjust the look of resulting graph.

Details

S3 method plot for class listofindex: -Normal type plot means, standard deviations, ranges and confidence intervals of T-statistics. -Simple_range type plot means, standard deviations and range of T-statistics -Simple type plot T-statistics for each site and traits and the mean confidence intervals by traits -Barplot type plot means, standard deviations and confidence intervals of T-statistics in a barplot fashion -Bysites type plot each metrics for each sites -Bytraits type plot each metrics for each traits

Value

None; used for the side-effect of producing a plot.

Author

Adrien Taudiere

Examples

  data(finch.ind)

  res.finch <- Tstats(traits.finch, ind.plot = ind.plot.finch, 
  sp = sp.finch, nperm = 9, print = FALSE)
#> Warning: This function exclude 1137 Na values

  if (FALSE) { # \dontrun{
    #### Use a different regional pool than the binding of studied communities
    #create a random regional pool for the example
  
    reg.p <- rbind(traits.finch, traits.finch[sample(1:2000,300), ])
  
    res.finch2 <- Tstats(traits.finch, ind.plot = ind.plot.finch, 
      sp = sp.finch, reg.pool=reg.p, nperm = 9, print = FALSE)  
      
      plot(as.listofindex(list(res.finch,res.finch2)))
    
    
      #### Use a different regional pool for each communities
    #create a random regional pool for each communities for the example
    list.reg.p <- list(
    traits.finch[sample(1:290,200), ], traits.finch[sample(100:1200,300), ], 
    traits.finch[sample(100:1500, 1000), ], traits.finch[sample(300:800,300), ],
    traits.finch[sample(1000:2000, 500), ], traits.finch[sample(100:900, 700), ] )

    # Warning: the regional pool need to be larger than the observed communities
    table(ind.plot.finch)
    # For exemple, the third community need a regional pool of more than 981 individuals
    
    res.finch3 <- Tstats(traits.finch, ind.plot = ind.plot.finch, 
      sp = sp.finch, reg.pool=list.reg.p, nperm = 9, print = FALSE)  
      
      plot(as.listofindex(list(res.finch, res.finch2, res.finch3)))  
  } # }