Plot the results of the leave-one-out analysis.

plot_loo(
  x,
  optima = TRUE,
  climate = x$parameters$climate[unlist(lapply(x$reconstructions, function(y)
    return("loo" %in% names(y))))],
  taxanames = x$inputs$taxa.name,
  save = FALSE,
  filename = "Diagram_loo.pdf",
  as.png = FALSE,
  png.res = 300,
  width = 3.54,
  height = 9,
  yax_incr = NA,
  bar_width = diff(range(x$inputs$x))/length(x$inputs$x),
  xlim = NA,
  tickAtSample = FALSE,
  sort = NA,
  filter = 0,
  col_pos = "black",
  col_neg = "grey80",
  title = NA
)

Arguments

x: A data frame of the data to plot (first column with age or depth) and the taxa in the following columns. x can also be a crestObj.
optima: A boolean to indicate whether to plot the optimum (TRUE) or the mean (FALSE) estimates.
climate: Climate variables to be used to generate the plot. By default all the variables are included.
taxanames: A list of taxa to use for the plot (default is all the recorded taxa).
save: A boolean to indicate if the diagram should be saved as a pdf file. Default is FALSE.
filename: An absolute or relative path that indicates where the diagram should be saved. Also used to specify the name of the file. Default: the file is saved in the working directory under the name 'Diagram_loo_climate.pdf'.
as.png: A boolean to indicate if the output should be saved as a png. Default is FALSE and the figure is saved as a pdf file.
png.res: The resolution of the png file (default 300 pixels per inch).
width: The width of the output file in inches (default 3.54in ~ 9cm).
height: The height of the output file in inches (default 9in ~ 23cm).
yax_incr: Graphical parameters describing the increment size on the y-axis (default 5).
bar_width: Width of the bars of the barplot (default 1).
xlim: The range covered by the x-axis. Can be adjusted to get round numbers on the x-axis. If smaller than the range covered by the data, the data will be truncated (default: range of the data).
tickAtSample: Boolean that indicates whether a tick mark should be added on the x-axis at the location of each sample (default TRUE).
sort: A string to sort the order of the taxa from the highest to lowest anomalies (sort='incr') or from the lowest to highest (sort='decr'). Use the default value NA to keep the taxa unsorted.
filter: A threshold value that determines the mean absolute anomaly value required for the taxon to be plotted (default 0 means that all taxa are plotted)
col_pos: Graphical parameter for the barplot. Colour of all the positive values (default black).
col_neg: Graphical parameter for the barplot. Colour of all the negative values (default grey80).
title: Name to be added on top of the plot (default NA).

Value

When used with a crestObj, it returns the average leave-one-out values for each selected taxa

Examples

if (FALSE) {
  data(crest_ex)
  data(crest_ex_pse)
  data(crest_ex_selection)
  reconstr <- crest(
    df = crest_ex, pse = crest_ex_pse, taxaType = 0,
    climate = c("bio1", "bio12"), bin_width = c(2, 20),
    shape = c("normal", "lognormal"),
    selectedTaxa = crest_ex_selection, dbname = "crest_example"
  )
  reconstr <- loo(reconstr)
}
## example using pre-saved reconstruction obtained with the previous command.
data(reconstr)
loo_vals <- plot_loo(reconstr, yax_incr=c(0.5, 50), bar_width=0.8,
                     col_pos=c('blue','cornflowerblue'),
                     col_neg=c('red', 'goldenrod3'))