gradient_change: Visualise change in (predicted) response over diversity gradient

Description

A scatter-plot of the predicted response (or raw response) over a diversity gradient for specific observations is shown. The points can be overlaid with `pie-glyphs` to show the relative proportions of the compositional variables. The average change in any user-chosen variable over the chosen diversity gradient can also be shown using the `y_var` parameter.
This is a wrapper function specifically for statistical models fit using the DI() function from the DImodels R package and it implicitly calls gradient_change_data followed by gradient_change_plot. If your model object isn't fit using DImodels, the associated data and plot functions can instead be called manually.

Usage

gradient_change(
  model,
  data = NULL,
  gradient = c("richness", "evenness"),
  add_var = list(),
  plot = TRUE,
  average = TRUE,
  y_var = ".Pred",
  pie_data = NULL,
  pie_colours = NULL,
  pie_radius = 0.25,
  points_size = 3,
  facet_var = NULL,
  nrow = 0,
  ncol = 0
)

Value

A ggmultiplot (ggplot if single plot is returned) class object or data-frame (if `plot = FALSE`)

Arguments

model: A Diversity Interactions model object fit by using the DI() function from the DImodels package.
data: A dataframe specifying communities of interest for which user wants to visualise the gradient. If left blank, the data used to fit the model will be used.
gradient: Diversity gradient to show on the X-axis, one of "richness" or "evenness". Defaults to "richness". See `Details` for more information.
add_var: A list specifying values for additional predictor variables in the model independent of the compositional predictor variables. This could be useful for comparing the predictions across different values for a non-compositional variable. If specified as a list, it will be expanded to show a plot for each unique combination of values specified, while if specified as a data-frame, one plot would be generated for each row in the data and they will be arranged in a grid according to the value specified in `nrow` and `ncol`.
plot: A boolean variable indicating whether to create the plot or return the prepared data instead. The default `TRUE` creates the plot while `FALSE` would return the prepared data for plotting. Could be useful for if user wants to modify the data first and then call the plotting function manually.
average: A boolean value indicating whether to plot a line indicating the average change in the predicted response with respect to the variable shown on the X-axis. The average is calculated at the median value of any variables not specified.
y_var: A character string indicating the column name of the variable to be shown on the Y-axis. This could be useful for plotting raw data on the Y-axis. By default has a value of ".Pred" referring to the column containing model predictions.
pie_data: Showing all points on the graph as pie-glyphs could be resource intensive. Hence a subset of data-frame specified in `data`, can be specified here to visualise only specific points as pie-glyphs.
pie_colours: A character vector specifying the colours for the slices within the pie-glyphs.
pie_radius: A numeric value specifying the radius (in cm) for the pie-glyphs.
points_size: A numeric value specifying the size of points (when pie-glyphs not shown) shown in the plots.
facet_var: A character string or numeric index identifying the column in the data to be used for faceting the plot into multiple panels.
nrow: Number of rows in which to arrange the final plot (when `add_var` is specified).
ncol: Number of columns in which to arrange the final plot (when `add_var` is specified).

Details

Currently two diversity gradients are supported

Richness: A metric describing the number of non-zero compositional variables in an observation.
Evenness: A metric quantifying the relative abundances of all compositional variables in an observation. Defined as $$(2s/(s-1)) \sum_{i, j = 1; i < j}^{s}{p_i * p_j}$$ where $s$ is the total number of compositional variables and $p_i$ and $p_j$ are the proportions of the variables $i$ and $j$. See Kirwan et al., 2007 <tools:::Rd_expr_doi("doi:10.1890/08-1684.1")> and Kirwan et al., 2009 <tools:::Rd_expr_doi("doi:10.1890/08-1684.1")> for more information.

Here's a small example of how these metrics are calculated for a few observations. Suppose we have four compositional variables (i.e. $s = 4$) and have the following three observations

A = (0.5, 0.5, 0, 0)
B = (0.25, 0.25, 0.25, 0.25)
C = (1, 0, 0, 0)

The richness values for these three observations would be as follows

A = 2 (Since two of the four compositional variables were non-zero)
B = 4 (Since all four compositional variables were non-zero)
C = 1 (Since one of the four compositional variables were non-zero)

The evenness values would be calculated as follows

A = $2*4/(4-1)*(0.5*0.5+0.5*0+0.5*0+0.5*0+0.5*0+0*0) = 0.67$
B = $2*4/(4-1)*(0.25*0.25+0.25*0.25+0..25*0.25+0.25*0.25+0.25*0.25+0.25*0) = 1$
C = $2*4/(4-1)*(1*0+1*0+1*0+0*0+0*0+0*0) = 0$

Examples

Run this code

## Load DImodels package to fit the model
library(DImodels)
library(dplyr)

## Load data
data(sim4)
sim4 <- sim4 %>% filter(treatment == 50)

## Fit DI model
mod <- DI(prop = 3:8, DImodel = "AV", data = sim4, y = "response") %>%
         suppressWarnings()

## Create visualisation

## By default, 'richness' is the gradient and communities from the
## raw data are used to calculate average response
gradient_change(model = mod)

## Specify custom data
gradient_change(model = mod, data = sim4 %>% filter(richness <= 4))

## Create plot for all equi-proportional communities at a
## given level of richness
plot_data <- get_equi_comms(6, variables = paste0("p", 1:6))
gradient_change(model = mod, data = plot_data)

## Can also plot average response across evenness and
## change colours of the pie-slices using `pie_colours`
gradient_change(model = mod, gradient = "evenness",
                pie_colours = c("darkolivegreen1", "darkolivegreen4",
                                "orange1", "orange4",
                                "steelblue1", "steelblue4"))

## Manually specify only specific communities to be shown as pie-chart
## glyphs using `pie_data` and `facet_var` to facet the plot on
## an additional variable.
gradient_change(model = mod,
                pie_data = sim4 %>% filter(richness %in% c(1, 6)),
                facet_var = "treatment")

## Use `add_var` to add additional variables independent of the compositions
## Multiple plots will be produced and can be arranged using nrow and ncol
## Create plot arranged in 2 columns
# \donttest{
gradient_change(model = mod,
                data = sim4[, -2],
                add_var = list("treatment" = c(50, 250)),
                pie_data = sim4[, -2] %>% filter(richness %in% c(1, 6)),
                ncol = 2)
# }

## Specify `plot = FALSE` to not create the plot but return the prepared data
head(gradient_change(model = mod, plot = FALSE,
                     pie_data = sim4 %>% filter(richness %in% c(1, 6)),
                     facet_var = "treatment"))

Run the code above in your browser using DataLab