rEDGE

Package to calculate EDGE scores and more phylogenetic-based indicators in R

Documentation of website under current development…

The EDGE index

The EDGE index is a metric that aims to prioritize species’ conservation bsed on both theis phylogenetic singularity (i.e. ED, Evolutionaty Distinctiveness) and their extinction risk (GE, Globally Endangered). Based on this idea, several methods have been developed in order to calculate individual EDGE scores.

To illustrate the differences among methods ant their implementationn within rEDGE package, we will see some examples using monotremates (i.e. platypus and echidna species).

EDGE1

Index based on Isaac et al., 2007. This first approach used evolutionary distinctiveness (ED) and a transformation of extinction risk (GE) in which each IUCN Red List category is twice as probable of becoming extinct. The EDGE score is calculated ussing the following formula:

EDGE = log(1+ED)+GE∗log(2)

To calculate this index for monotremates, we just have to use the calculate_EDGE1 function specifying uot phylogenetic tree, and a table including all the tree’s species (in a clomn named species, and their respective IUCN category in a column named RL.cat). Note that all species must be included, so if there are species included on the tree and not evaluated, make sure to include them on the table wit a “NE” category.

EDGE1 <- calculate_EDGE1(tree = monotreme.tree, 
                         table = monotreme.table, 
                         sort.list = T # to get the list sorted by decreasing EDGE value
                         )

knitr::kable(EDGE1)

species	RL.cat	ED	EDGE
Zaglossus_attenboroughi	CR	14.23723	5.496331
Zaglossus_bruijnii	CR	14.23723	5.496331
Zaglossus_bartoni	VU	14.75253	4.143296
Ornithorhynchus_anatinus	NT	29.83242	4.121714
Tachyglossus_aculeatus	LC	18.04178	2.946636

EDGE2

In order to take into account the extinction probability of closely related taxa as well as uncertainty in the extinction probability of species, Gumbs et al., 2023 designed a new methodology, termed EDGE2.

In this new approach, a probabilty of extinction is sampled from a continuous distribution based on the IUCN Red List category, and ED2 and EDGE” values can be calculated (develop more thoroughly…).

EDGE2 <- calculate_EDGE2(tree = monotreme.tree, 
                         table = monotreme.table, 
                         sort.list = T, # to get the list sorted by decreasing EDGE value
                         verbose = F)

knitr::kable(EDGE2)

species	RL.cat	TBL	pext	ED	EDGE
Zaglossus_bruijnii	CR	8.147095	0.9999000	10.69954	10.6984729
Zaglossus_attenboroughi	CR	8.147095	0.9905879	10.72354	10.6226066
Ornithorhynchus_anatinus	NT	29.832422	0.1496076	29.83242	4.4631576
Zaglossus_bartoni	VU	9.177698	0.2818624	14.61081	4.1182375
Tachyglossus_aculeatus	LC	14.111567	0.0350753	18.50054	0.6489122

As this EDGE score is iteration dependant (i.e. there is a random factor in the sampling of extinction probabilty), a set of EDGE2 values can be calculated and averaged posteriorly. This multiple calculation is performed by calculate_EDGE2_multiple function, which allows to parallelize in order to speed computation times. In this example we are calculating EDGE scores 50 times and averaging the results after.

EDGE2mult <- calculate_EDGE2_multiple(tree = monotreme.tree, 
                                      table = monotreme.table, 
                                      n.iter = 50,
                                      parallelize = TRUE,
                                      n.cores = 10
                                      )
#> [1] "Seed has been set to: 39380337"


# Now we summarise table results...
EDGE2mult_summ <- EDGE2mult |> 
  bind_rows()  |> 
  group_by(species) |> 
  summarise(RL.cat = paste0(unique(RL.cat)),
            TBL  = mean(TBL ),
            pext = mean(pext),
            ED   = mean(ED  ),
            EDGE = mean(EDGE) ) |> 
  arrange(desc(EDGE))

knitr::kable(EDGE2mult_summ)

species	RL.cat	TBL	pext	ED	EDGE
Zaglossus_bruijnii	CR	8.147095	0.9240231	10.34608	9.5572687
Zaglossus_attenboroughi	CR	8.147095	0.9180105	10.35906	9.5082837
Ornithorhynchus_anatinus	NT	29.832422	0.1284080	29.83242	3.8307210
Zaglossus_bartoni	VU	9.177698	0.2408466	14.02165	3.3645653
Tachyglossus_aculeatus	LC	14.111567	0.0493775	17.30895	0.8474662