deconstruct_modes: Deconstruct a multimodal gambin model fit

Description

Deconstruct a multimodal gambin model fit by locating the modal octaves and (if species classification data are provided) determining the proportion of different types of species in each octave.

Usage

deconstruct_modes(fit, dat, peak_val = NULL, abundances = "abundances",
  species = "species", categ = NULL, plot_modes = TRUE,
  col.statu = NULL)

Arguments

fit

A gambin model fit where the number of components is greater than one (see fit_abundances).

dat

A matrix or dataframe with at least two columns, including the abundance data used to fit the multimodal gambin model and the species names. An optional third column can be provided that contains species classification data.

peak_val

A vector of of modal octave values. If peak_val = NULL, the modal octave values are taken from the model fit object.

abundances

The name of the column in dat that contains the abundance data (default = "abundance").

species

The name of the column in dat that contains the species names (default = "species").

categ

Either NULL if no species classification data are provided, or the name of the column in dat that contains the species classification data.

plot_modes

A logical argument specifying whether a barplot of the model fit with highlighted octaves should be generated. If categ = FALSE a barplot is produced whereby just the modal octaves are highlighted in red. If categ = TRUE a barplot is produced whereby the bar for each octave is split into n parts, where n equals the number of species categories.

col.statu

A vector of colours (of length n) for the split barplot, where n equals the number of species categories.

Value

An object of class deconstruct. The object is a list with either two or three elements. If categ = NULL, the list has two elements: 1) 'Peak_locations', which contains the modal octave values, and 2) 'Species_per_octave', which is a list where each element contains the species names in an octave. If categ != NULL, the returned object has a third element: 3) 'Summary_table', which contains a dataframe (frequency table) with the numbers of each category of species in each octave.

Details

The function enables greater exploration of a multimodal gambin model fit. If no species classification data are available (i.e. categ = NULL) the function returns the modal octaves of the n-component distributions and the names of the species located in each octave. If plot_modes = TRUE a plot is returned with the modal octaves highlighted in red. If species classification data are provided the function also returns a summary table with the number of each species category in each octave provided. The user can then use these data to run different tests to test whether, for example, the number of species in each category in the modal octaves is significantly different than expected by chance. If plot_modes = TRUE a split barplot is returned whereby each bar (representing an octave) is split into the n species categories.

Species classification data should be of type character (e.g. native or invasive).

Occasionally, some of the component distributions in a multimodal gambin model fit have the same modal octave; this is more common when fitting the 3-component model. When this occurs a warning is produced, but it is not a substantive issue.

Examples

Run this code

# NOT RUN {
data(categ)
fits2 = fit_abundances(categ$abundances, no_of_components = 2)
#without species classification data
deconstruct_modes(fits2, dat = categ, peak_val = NULL, abundances = "abundances", 
species = "species", categ = NULL, plot_modes = TRUE)
#with species classification data
deconstruct_modes(fits2, dat = categ, categ = "status", col.statu = c("green", "red", "blue"))
#manually choose modal octaves
deconstruct_modes(fits2, dat = categ, peak_val = c(0,1))
# }

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