crestr (version 1.2.1)

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

Description

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

Usage

plot_loo(
  x,
  optima = TRUE,
  climate = x$parameters$climate,
  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))/50,
  xlim = NA,
  tickAtSample = FALSE,
  sort = NA,
  filter = 0,
  col_pos = "black",
  col_neg = "grey80",
  title = NA
)

Value

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

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).

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'))