Diagnostic Plots in funbiogeo • funbiogeo

funbiogeo contains many plotting functions. They have multiple goals: (1) propose good default plots to inspect and represent your data, (2) provide easy plotting methods for complex objects (automatically display maps from spatial objects), and (3) provide plotting methods for computed functional diversity metrics in other packages. This vignette explains in detail all plotting functions available in funbiogeo, how to use them and how to interpret them.

Some of these plotting functions use different data inputs and some of them can deal with species categorization, i.e. displaying information by each category of species (family, order, endemism status, etc.). We detail the standard needed inputs in the table below, the “Additional input” column represents needed input that are not the other standard tables specified by the other columns.

A table of available plotting functions in `funbiogeo` ordered alphabetically with their required arguments. The “Additional input” column reflects the need for other argument that are not of the standard object type.
Function name	Site x species	Species x traits	Site x locations	Species category	Additional input
`fb_plot_distribution_site_trait_coverage()`	✅	✅	❌	✅	❌
`fb_plot_number_sites_by_species()`	✅	❌	❌	❌	❌
`fb_plot_number_species_by_trait()`	❌	✅	❌	✅	❌
`fb_plot_number_traits_by_species()`	❌	✅	❌	✅	❌
`fb_plot_site_environment()`	❌	❌	✅	❌	✅
`fb_plot_site_traits_completeness()`	✅	✅	❌	✅	❌
`fb_plot_species_traits_completeness()`	❌	✅	❌	✅	❌
`fb_plot_species_traits_missingness()`	❌	✅	❌	✅	❌
`fb_plot_trait_combination_frequencies()`	❌	✅	❌	✅	❌
`fb_plot_trait_correlation()`	❌	✅	❌	✅	❌
`fb_map_raster()`	❌	❌	❌	❌	✅
`fb_map_site_data()`	❌	❌	✅	❌	✅
`fb_map_site_traits_completeness()`	✅	✅	✅	❌	❌

Let’s first load the package and example datasets included in the funbiogeo.

library("funbiogeo")
library("sf")
#> Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE

data("site_locations")
data("site_species")
data("species_traits")

Naming Convention

Like in the rest of the funbiogeo package, the functions are named following certain conventions. For one, to avoid any collision with other packages all the functions are prefixed with fb_. Second all plotting functions begin with either fb_plot_*(), when they are regular plots, or fb_map_*() when they plot maps.

The function names in funbiogeo are generally long to be as specific and clear as possible. So in case of doubt re-read the function name, and what it should represent should be clear from the name.

Regular Plots

In this section we will describe what we call “regular plots”, i.e. plots of non-spatial objects (density plots, bivariate plots, lollipop charts, heatmaps, etc.). We made this distinction because maps have their own specific challenges. All the default regular plots proposed in funbiogeo are quite specific to the data. In each of the section below we’ll summarize what the plots is about, what are the needed arguments, and how to interpret the output.

The function are all described in their specific subsections in alphabetical order.

Distribution of trait coverages across sites

Visualizing the trait coverage of all sites can help isolate which traits may show consistently low coverage. Also this can help notice if some groups of sites have higher coverage for certain traits than for others.

You can plot this using the fb_plot_distribution_site_trait_coverage() function. It takes two arguments: site_species the site by species data.frame and species_traits the species by traits data.frame. Note that internally the function uses ggridges to plot the distributions. This package is thus needed to run this function.

Example:

fb_plot_distribution_site_trait_coverage(site_species, species_traits)
#> Loading required namespace: ggridges
#> Picking joint bandwidth of 0.00988

We see the distribution of species coverage per site (along the x-axis) for each trait (along the y-axis) and with all traits taken together (shown at the top of the top on the line all_traits). The proportions on the y-axis labels are the average coverage observed for this trait. So for example, considering only adult body mass as a trait would mean that we would achieve an average coverage of 95.3%, meaning that on average across all sites 95.3% of species are covered. We can compare this to the trait max_longevity which corresponds to the maximum longevity of the species. We see that the average trait coverage across all sites is 82.1%. We see that the distribution however is rather wide, with some sites showing a coverage of around 90% (the large bump), while some sites are close to 62% coverage.

This plot considers the distribution of species across sites instead of focusing only on the species by traits data.frame. This maybe useful to realize, for example, that the traits of a species occurring very rarely are missing this wouldn’t necessarily translate in low site-level trait coverage.

Plotting the number of sites by species

The function fb_plot_number_sites_by_species() allows to explore the site by species data.frame. It shows the number (and proportion) of sites occupied by each species. Its first argument site_species, the site by species data.frame is necessary while the second one threshold_sites_proportion, a target proportion of sites coverage, is optional.

fb_plot_number_sites_by_species(site_species)
#> There are more than 30 species, the y-axis will label the position of 30 evenly spaced species (along their prevalence)

The function outputs a dotchart. The number of occupied sites per species is indicated at the bottom x-axis, while the top x-axis represents the proportion of occupied sites. The left y-axis label species names (in parenthesis) and their rank by increasing prevalence. Note that for readability constraints, only a limited number of species are labeled on the y-axis, but they are all displayed as dots on the plot.

Adding the second argument threshold_sites_proportion displays a vertical bar at the target proportion of sites to see how many species occupy more or less than the given proportion of sites.

Let’s say we want to see the species present in at least 40% of the sites:

fb_plot_number_sites_by_species(site_species, threshold_sites_proportion = 0.4)
#> There are more than 30 species, the y-axis will label the position of 30 evenly spaced species (along their prevalence)

The threshold bar helps us get a sense of how many species are present in at least 40% of the sites. It also displays the corresponding number of sites.

Plotting the number of species per trait

One way to look at the species by traits data.frame is to look at number of species with non-missing trait values for each trait. The fb_plot_number_species_by_trait() function does exactly that. Its first argument species_traits, the species by traits data.frame, is necessary while the second one threshold_species_proportion, a target proportion of species coverage, is optional.

fb_plot_number_species_by_trait(species_traits)

The function outputs a lollipop chart. On the bottom x-axis there is the number of species covered by the given trait (the top x-axis represents the proportion of species, which is directly proportional). The y-axis represents each trait. The dot represents the actual coverage observed with the corresponding proportion of species written on top. With this figure we see that 82.6% of the species have a non-missing adult body mass in the species by trait data.frame, while only 54.4% have a non-missing maximum longevity.

Adding the second argument threshold_species_proportion displays a vertical bar at the target proportion to easily target traits covering a certain proportion of species. Let’s say we want to see traits available for at least 70% of the species:

fb_plot_number_species_by_trait(species_traits, threshold_species_proportion = 0.7)

The red dashed vertical line shows the corresponding species coverage with labels indicating the proportion and corresponding number of species (n = 104).

Plotting the number of traits per species

You can also display the number of traits available per species. Showing it for each species would be quite difficult to read, so we decided instead to represent the number of species having given number of known traits. Also, because most trait ecologists are interested in multiple traits, we considered nested proportions of traits: considering the number of species covered by at least one trait, at least two, etc.

To represent such a plot you can use the function fb_plot_number_traits_by_species(), it uses two arguments. The first species_traits is the species by traits data.frame. The second argument is threshold_species_proportion which is optional and corresponds to a certain threshold proportion of species, so that a line can be added to the plot.

Using it on the included dataset gives:

fb_plot_number_traits_by_species(species_traits)

The x-axis represents the number of species concerned (bottom x-axis displays the actual number of species, while top x-axis displays the corresponding proportion of species). The y-axis shows the number of each traits. Note that the categories are nested: the set of species with at least 1 trait contains the set of species with at least 2 traits, and so on and so forth. By definition all species have 0 or more known traits, but we show that in the plot as a reference to see how the proportion decreases with increasing number of traits. The proportion is shown as text above each dot representing it. So for example, there are 62.4% species with at least 4 traits.

This plot does not tell us if all species with at least 4 traits share the same trait combination (there are multiple 4 trait combinations), but it’s a first indication.

Let’s say we’re interested in combinations of traits with at least 50% species covered. We can use the second argument to show it:

fb_plot_number_traits_by_species(species_traits, threshold_species_proportion = 0.5)

Adding this argument displays a vertical bar at the target proportion of species to easily target number of traits covering a certain proportion of species. The red dashed vertical line shows the corresponding species coverage with labels indicating the proportion and corresponding number of species (n = 74).

Plotting environmental position of sites

To see if our sites are biased environmentally it can be nice to locate them along environmental variables compared to a full region. For the sake of simplicity we can focus on two variables against which to compare our sites to a region. That is what the fb_plot_site_environment() function does. It has four arguments: the first one, site_locations, provides the locations of sites as an sf object, environment_raster is a terra raster object, the next two arguments are first_layer and second_layer which are the names of the two variables to be extracted from environment_raster to make our plot.

From the included dataset we can represent the first 6 sites along total annual precipitation and mean annual temperature over the full region:

# Create the environmental rasters
prec <- system.file("extdata", "annual_tot_prec.tif", package = "funbiogeo")
tavg <- system.file("extdata", "annual_mean_temp.tif", package = "funbiogeo")

layers <- terra::rast(c(tavg, prec))

# Make plot (show environmental position of 6 first sites)
fb_plot_site_environment(head(site_locations), layers)
#> Warning: Removed 49503 rows containing missing values or values outside the scale range
#> (`geom_point()`).

The plot shows the first selected layer as the x-axis and the second one as the y-axis. The environmental position of the sites are displayed using the big blue dots, while the light gray pixels are all the environmental variables extracted from the provided environmental raster.

This figure can show us that the first six sites are actually lower in temperature and higher in annual precipitation than most other places in our environmental rasters.

Plotting trait coverage for all sites

To select appropriate sites and traits, we can visualize the trait coverage per site and per trait. This is exactly what is done by fb_plot_site_traits_completeness() which takes site_species, the site by species data.frame, and species_traits, the species by traits data.frame, as arguments.

We can use it with the included dataset as an example:

fb_plot_site_traits_completeness(site_species, species_traits)

The plot shows the trait along the x-axis (and their average coverage across all sites in their labels) and sites along the y-axis. Each thin horizontal line represents a site. The color indicates the coverage for the trait in each column. Note that for readability reasons the color scale has been discretized from 0 to 100% coverage. Traits are ranked in decreasing average coverage. The last column all_traits contains the coverage for all traits taken together.

With this figure we can see that all sites have over 80% coverage with both adult body mass and litter size.

Plotting trait coverage per species

To select appropriate traits, we can visualize the trait coverage per species. This is done by fb_plot_species_traits_completeness() which takes species_traits, the species by traits data.frame, for sole argument.

We can use it with the included dataset as an example:

fb_plot_species_traits_completeness(species_traits)

This figure visualizes directly the species by trait data.frame. The x-axis displays the different traits, ranked from left to right in decreasing coverage order (as indicated in the x-axis labels). The last column all_traits considers all traits taken together. The y-axis represents species in decreasing coverage order from bottom to top. Each cell thus represents the trait for a species: blue if the trait is known and red if it is missing.

From this plot we see that a significant proportion of species have missing traits and that even the most non-missing traits, adult body mass, is only known for 82.6% of the species.

Plotting number of species with missing traits

Maybe you’re rather interested in plotting the number of species with known (or missing) traits in your dataset. This plot is an alternative to the one from the previous section. It can be done through fb_plot_species_traits_missingness() which takes species_traits, the species by traits data.frame, for argument as well as all_traits to know if an additional row should be used to display a summary for all traits taken together.

fb_plot_species_traits_missingness(species_traits, all_traits = TRUE)

The plot displays the number of species with known and missing traits. It shows each trait in separate line as a proportional bar chart with the total numbers included within each bar.

Here we see that 53 species have all of their traits known while 96 don’t. Adult body mass is known for 123 species and missing for 26.

Displaying traits combinations

Looking at the traits coverage for each species continuously maybe impractical or difficult. For example, when trying to display thousands of species or when the trait coverage varies widely across species. One way to reduce the size of the analyzed (and thus visualized) dataset is instead to count at which frequency appear the combinations of present/missing traits.

This is done by fb_plot_trait_combination_frequencies() which takes two arguments: species_traits, the species by traits data.frame, and order_by (equals to either "number", the default option, or "complete"), which influences the order of the plot (more details below).

We can use it with the included dataset as an example:

fb_plot_trait_combination_frequencies(species_traits)

The x-axis represents individual traits ranked in alphabetical order from left to right. The y-axis represents different combinations. The labels on the y-axis show both the number and the frequency of each combination. When the cell is blue it means that the trait is present, when it is red it means the trait is missing. By default the combinations are ordered by increasing number from top to bottom, with the most numerous combinations of trait presences at the very bottom of the graph.

With this graph we can see that we have exactly 53 species (35.6% of the total number of species provided) have all their traits present, while 21 species (14.1%) have not a single trait in the dataset.

If we change order_by to "complete", the combinations are ordered instead by the number of trait presents among them:

fb_plot_trait_combination_frequencies(species_traits, order_by = "complete")

The most complete combinations are shown at the bottom, while the combinations with most missing traits are at the top.

Displaying traits correlations

Most of the plot functions in funbiogeo show traits independently of one another. However, for functional biogeography analyses, trait correlations maybe very relevant. This is exactly what is done by fb_plot_trait_correlation(). It takes as first needed argument species_traits, the species by traits data.frame. The other arguments are optional and will be passed to stats::cor().

Note that the function only works with numerical traits and with complete observations. It silently removes any species that has any NA.

With the included dataset as an example:

fb_plot_trait_correlation(species_traits)

Both x- and y-axes represent the different traits. At their intersection are shown squared that are colored in function of their correlation coefficient (purple means close to -1 correlation while brown means close to 1, white means close to 0). The correlation coefficients are also displayed in the middle of this square.

With this visualization we can see that adult body mass and gestation length are quite highly correlated (cor = 0.7), while diet breadth is correlated with no other trait.

Maps

Map functions in funbiogeo are here to provide good default visualization leveraging the spatial information of sites. We know that producing map in R is challenging. That’s why we provide these helper functions. Of course, these functions are all basics and you either have to customize them by adding ggplot2 commands to the returned plots, or to look at their code to produce similar plots in the way you want.

For example, the functions do not display background maps because it would be too complex to accommodate for all use cases between quite localized sites up to global level analyses.

Note that all maps are always in the Coordinate Reference System of the provided site_locations object. You can also tweak that by adding a custom ggplot2::coord_sf() call.

Mapping traits coverage of sites

The function fb_map_site_traits_completeness() maps the trait coverage (proportion of species, weighted by relative abundance if relevant, with known trait values) of each site for all traits.

It takes three arguments: site_locations (spatial locations of sites), site_species (site by species data.frame), and species_traits (species by traits data.frame).

If we use the included dataset in funbiogeo it gives:

fb_map_site_traits_completeness(site_locations, site_species, species_traits)

It displays maps of the sites, colored by their trait coverage. Each facet represents a different trait while the all_traits facet consider all traits together.

From this plot we can see that on average the South of Western Europe is less covered by traits than the North of Western Europe. It may be an indication of higher species richness in the South compared to the North which makes achieving high coverages more difficult. Furthermore, we can see that a site in the Netherlands has 0% coverage of diet breadth. This is most likely the sign of sign of low species richness with an absence of diet breadth for those species.

Mapping arbitrary site data

To be the most flexible possible, funbiogeo provides a function to map arbitrary site data whether quantitative or qualitative with the fb_map_site_data() function. The first argument it takes is site_locations, the spatial locations of sites as an sf object, the second argument is site_data which is a data.frame containing a "site" column and data in additional columns, the third and last required argument is selected_col which should be the name of the column provided in the site_data data.frame that is going to be used as a variable to display. All three arguments are required.

For example, if we want to get a map of species richness of the included dataset we can do the following:

# Compute Species Richness
site_rich <- fb_count_species_by_site(site_species)

# Map of Species Richness
fb_map_site_data(site_locations, site_rich, "n_species")

From this map, we can for example see that the Northern part of our dataset is less species-rich than the center or the South.

Now imagine we want to display the category of sites which be “Testing” or “Training”, depending on which set they belong to. We can use the following to display the map:

# Generate categories
site_cat <- data.frame(
  site = site_species$site,
  set  = sample(c("Testing", "Training"), nrow(site_species), replace = TRUE)
)

# Display them
fb_map_site_data(site_locations, site_cat, "set")

Mapping site rasters

Mapping rasters can be quite cumbersome with R. funbiogeo provides a generic function to map them with fb_map_raster(). It only needs as first argument a terra SpatRaster object. It can be very useful when visualizing environmental layers for example. The function will display the raster in the provided projection.

For example:

# Getting the raster
tavg <- system.file("extdata", "annual_mean_temp.tif", package = "funbiogeo")
tavg <- terra::rast(tavg)

# Mapping the raster
fb_map_raster(tavg)