Species correlations — rsp.cor • respeciate

Functions for studying relationships between species in respeciate data sets.

rsp_cor_species generates a by-species correlation matrix of the supplied respeciate data sets.

rsp_cor_species(
  rsp,
  min.n = 3,
  cols = c("#80FFFF", "#FFFFFF", "#FF80FF"),
  na.col = "#CFCFCF",
  heatmap.args = TRUE,
  key.args = TRUE,
  report = "silent"
)

Arguments

rsp: respeciate object, a data.frame of respeciate profiles.
min.n: numeric (default 3), the minimum number of species measurements needed in a profile for the function to use it in correlation calculations. Here, it should be noted that this does not guarantee the three matched pairs of measurements needed to calculate a correlation coefficient because not all profiles contain all species, so there may still be insufficient overlap on a case-by-case basis.
cols: a series of numeric, character or other class values that can be translated into a color gradient, used to color valid cases when generating plots and color keys, default c("#80FFFF", "#FFFFFF", "#FF80FF") equivalent to cm.colors output.
na.col: numeric, character or other class that can be translated into a single color, used to color NAs when generating plots and color keys, default grey "#CFCFCF".
heatmap.args: logical or list, heat map settings. Options include TRUE (default) to generate the heat map without modification; FALSE to not plot it; or a list of heat map options to alter the plot default appearance. The plot, a standard heat map with the dendrograms removed, is generated using heatmap, so see associated documentation for valid options.
key.args: logical or list, color key settings if plotting the correlation matrix heat map. Options include TRUE (default) to generate the key without modification; FALSE to not include the key; or a list of options to alter the key appearance.
report: logical or character, the required function output. Options include: 'silent' (default), to return the correlation matrix invisibly; TRUE to return the matrix (visibly); and, FALSE to not return it.

Value

By default rsp_cor_species invisibly returns the calculated correlation matrix a plots it as a heat map, but arguments including heatmap and report can be used to modify function outputs.