Plot SES values against a variable

Plot standardized effect size values against a variable

Usage

plotSESvar(index.list, variable = NULL, ylab = "variable", 
  color.traits = NULL, val.quant = c(0.025, 0.975), resume = FALSE, 
  multipanel = TRUE)

Arguments

index.list

A list of index and the associate null models in the forme: list( index_1 = index_1_observed, index_1_nm = null.model.index_1 ,index_2 = index_2_observed, index_2_nm = null.model.index_2, ...).

variable

The variable against standardized effect sizes are plotted.

ylab

Label for the variable.

color.traits

A vector of colors corresponding to traits.

val.quant

Numeric vectors of length 2, giving the quantile to calculation confidence interval. By default val.quant = c(0.025,0.975) for a bilateral test with alpha = 5%.

resume

Logical value; resume = FALSE by default; Simplify the plot by plotting the mean and standard error for index value of multiple traits

multipanel

Logical value. If TRUE divides the device to shown several traits graphics in the same device.

Value

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

Author

Adrien Taudiere

See also

plot.listofindex; ses

Examples

  data(finch.ind)
  res.finch <- Tstats(traits.finch, ind.plot = ind.plot.finch, sp = sp.finch, 
  nperm = 9)
#> Warning: This function exclude 1137 Na values
#> [1] "creating null models"
#> [1] "8.33 %"
#> [1] "16.67 %"
#> [1] "25 %"
#> [1] "33.33 %"
#> [1] "41.63 %"
#> [1] "49.97 %"
#> [1] "58.3 %"
#> [1] "66.63 %"
#> [1] "74.93 %"
#> [1] "83.27 %"
#> [1] "91.6 %"
#> [1] "99.93 %"
#> [1] "calculation of Tstats using null models"
#> [1] "8.33 %"
#> [1] "16.67 %"
#> [1] "25 %"
#> [1] "33.33 %"
#> [1] "41.63 %"
#> [1] "49.97 %"
#> [1] "58.3 %"
#> [1] "66.63 %"
#> [1] "74.93 %"
#> [1] "83.27 %"
#> [1] "91.6 %"
#> [1] "99.93 %"
if (FALSE) { # \dontrun{
  par(mfrow = c(2,2))
  species.richness <- table(ind.plot.finch)
  plotSESvar(as.listofindex(list(res.finch)), species.richness, 
  multipanel = FALSE)

  #Same plot with resume = TRUE.
  
  par(mfrow = c(2,2))
  plotSESvar(as.listofindex(list(res.finch)), species.richness, 
  resume = TRUE, multipanel = FALSE)
  par(mfrow = c(1,1))
  } # }