Received: 22 June 2023 | Accepted: 8 November 2023

DOI: 10.1111/2041-210X.14259

RESEARCH ARTICLE

Generative spatial generalized dissimilarity mixed modelling

(spGDMM): An enhanced approach to modelling beta diversity

Philip A. White1,2 | Henry A. Frye3 | Jasper A. Slingsby4,5 | John A. Silander Jr3 |

Alan E. Gelfand6
1
Berry Consultants, Austin, Texas, USA; 2Department of Statistics, Brigham Young University, Provo, Utah, USA; 3Department of Ecology & Evolutionary
Biology, University of Connecticut, Storrs, Connecticut, USA; 4Department of Biological Sciences and Centre for Statistics in Ecology, Environment and
Conservation, University of Cape Town, Cape Town, South Africa; 5Fynbos Node, South African Environmental Observation Network, Cape Town, South Africa
and 6Department of Statistical Science, Duke University, Durham, North Carolina, USA

Correspondence
Philip A. White
Email: philip@berryconsultants.net
Funding information
National Science Foundation, Grant/
Award Number: DEB-1046328;
NASA Earth and Space Science and
Technology (FINESST), Grant/Award
Number: 80NSSC20K1659; NASA
BioSCape Award, Grant/Award Number:
80NSSC22K1383; National Research
Foundation, Grant/Award Number:
150926, 142438 and 118593
Handling Editor: Robin Boyd
Abstract
1. Turnover, or change in the composition of species over space and time, is one
of the primary ways to define beta diversity. Inferring what factors impact beta
diversity is not only important for understanding biodiversity processes but also
for conservation planning. At present, a popular approach to understanding the
drivers of compositional turnover is through generalized dissimilarity modelling
(GDM). We argue that the current GDM approach suffers several limitations and
provide an alternative modelling approach that remedies these issues.
2. We propose using generative spatial random effects models implemented in a
Bayesian framework. We offer hierarchical specifications to yield full regression
and spatial predictive inference, both with associated full uncertainties. The ap-
proach is illustrated by examining dissimilarity in three datasets: tree survey data
from Panama's Barro Colorado Island (BCI), plant occurrence data from southwest
Australia and plant abundance surveys from the Greater Cape Floristic Region
(GCFR) of South Africa. We select a best model using out-of-sample predictive
performance.
3. We find that the form of the best model differs across the three datasets, but our
models provide performance ranging from comparable to significant improve-
ment over GDMs. Within the GCFR, the spatial random effects play a more im-
portant role in the modelling than all the environmental variables.
4. We have proposed a model that provides several improvements to the current
GDM framework. This includes advantages such as a flexible spatially varying
mean function, spatial random effects that capture dependence unaccounted
for by explanatory variables, and spatially heterogeneous variance structure. All
these features are offered in a model that can adequately handle a large incidence

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium,
provided the original work is properly cited.
© 2023 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society.

214 | 
wileyonlinelibrary.com/journal/mee3 Methods Ecol Evol. 2024;15:214–226.

WHITE et al.
of total dissimilarity through ‘one-inflation’, as would be expected from highly bio-
diverse areas with steep turnover gradients.
KEYWORDS
biodiversity, coherent/generative models, hierarchical models, model comparison and
validation, spatial random effects, warping functions
1 | I NTRO D U C TI O N
Change in the composition of biotic assemblages in space and time is
important for revealing the ecological processes that structure and
maintain biodiversity spatially across landscapes, detecting biodi-
versity loss or change in the composition of assemblages, or tracking
global biodiversity change (Ferrier et al., 2020; Hoskins et al., 2020).
Such turnover is referred to as beta diversity and has been applied
to taxonomic, functional, phylogenetic and spectral measures of di-
versity (see, e.g. Graham & Fine, 2008; Schweiger & Laliberté, 2022;
Whittaker, 1960). Unfortunately, modelling beta diversity presents
many unique challenges and, while several methods have been pro-
posed, there are many issues that remain to be overcome. Here we
reformulate the generalized dissimilarity modelling (GDM) method
of Ferrier (2002) and Ferrier et al. (2007) and propose several sig-
nificant advances that should aid modelling of beta diversity and the
many applications it supports.
While beta diversity can be expressed as a single metric represent-
ing variation across multiple samples in a region (Whittaker, 1960), it
is more commonly expressed as differences in composition between
pairs of samples (Anderson et al., 2011). Modelling beta diversity
based on pairwise analyses requires a distance-based statistical
framework. Several approaches have been proposed (Anderson
et al., 2011), though each has its limitations or flawed assumptions.
Early efforts include the Mantel test of correlation between distance
matrices (Legendre, 1993), ordination of assemblages based on their
pairwise compositional differences, for example, non-metric multi-
dimensional scaling (NMDS; Prentice, 1977), and linear matrix re-
gression (Manly, 1986), where the level of difference between pairs
of assemblages is related linearly to differences in environment or
space.
Unfortunately, these properties are often not linear because:
(i) Most ecological dissimilarity measures are constrained to range
from 0, when assemblages are identical, to saturating at a maximum
value of 1, once pairs of assemblages are completely different. In
biodiverse regions, datasets may contain a high proportion of 1s,
which are not adequately explained by models based on standard
distributional assumptions. This is akin to the issue of 0-inflation
commonly faced in population and community modelling (Blasco-
Moreno et al., 2019). (ii) The rate of change in assemblage compo-
sition in relation to environmental variables can vary nonlinearly
along a gradient (Fitzpatrick et al., 2013; Oksanen & Tonteri, 1995),
which necessitates modelling explicitly in a spatial context (Ferrier
et al., 2007).
|
2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
215
Responding to issues of nonlinearity in relating beta diver-
sity to environmental gradients, Ferrier and colleagues developed
GDM (Ferrier, 2002; Ferrier et al., 2004, 2007). This approach was
argued as an extension of generalized linear modelling of pair-
wise distances and has become increasingly popular for analysing
compositional turnover (Mokany et al., 2022). GDM underpins the
calculation of several Global Biodiversity Change Indicators pro-
posed by the Group on Earth Observations Biological Observation
Network (GEO BON), which are used to support global initiatives
like the Intergovernmental Science-Policy Platform on Biodiversity
and Ecosystem Services (IPBES) and the Convention on Biological
Diversity's (CBD) Post-2020 Global Biodiversity Framework (Ferrier
et al., 2020; Hoskins et al., 2020). Unfortunately, GDM itself retains
some flaws and limitations, which could have consequential implica-
tions for global biodiversity monitoring and management. Here, we
highlight issues with the GDM method and then propose and imple-
ment a richer, generative modelling approach that is fully spatial. For
us, generative means coherent, that is, a process specification which
could have generated the observed data.
1.1 | A review and critique of generalized
dissimilarity modelling
Generalized dissimilarity modelling treats between-site dissimi-
larities (beta diversity measures) as the response of interest. In
the paper, we also use GDM to represent generalized dissimilarity
model. For two sites, between-site dissimilarities are calculated as
a function of community composition, considering differences in
the presence/absence of taxa (at some taxonomic level) and, for
some metrics, differences in their relative abundance. The GDM
imagines that dissimilarities are explained by differences between
monotonically warped environmental variables; the warping enables
differences between environmental variables to relate nonlinearly
to dissimilarity. Following Ferrier et al. (2007), GDM describes dis-
similarities using a linear combination of differences in monotone
transformations of a vector of site-level environmental covariates,
the latter denoted by X(s) where s ∈ , the study domain of interest.
In addition, they may employ a monotone transformation of spatial
distance to account for additional dissimilarity that is not effectively
explained by environmental variables.
( )
Adopting a dissimilarity measure for two sites, Z s, s′ , the GDM
does the following. It proposes to model a transformed/predicted
ecological mean distance, 𝜂 on R+, and then links it to the interval
 |
216
[ ]
0, 1 through 𝜇 = 1 − e−𝜂. It further suggests a scaled variance func-
tion proportional to 𝜇(1 − 𝜇). With this link and variance function,
iteratively re-weighted least squares (IRLS) fitting is implemented to
infer the parameters in the specification of 𝜂. The proposed form for
( )
𝜂 s, s′ is
( ) ( ( )) ∑
P
( ) ( ( ))
𝜂 s, s� = 𝛽 0 + h d s, s� + ∣ fp Xp (s) − fp Xp s� ∣ (1)
p=1
where h( ⋅ ) and fp ( ⋅ ) are unique monotone increasing functions for
distance and all the environmental covariates respectively. Ferrier
et al. (2007) specify h( ⋅ ) and fp ( ⋅ ) using I-spline basis functions with
positive coefficients, to ensure that the transformation of the environ-
mental covariate is monotone (Ramsay, 1988). The number and choice
of I-spline basis functions are supplied for each of the regressors indi-
vidually, before the IRLS fitting.
There are several features of this modelling/fitting approach that
raise cause for concern.
• First, there is no formal likelihood for the data. Fitting, using the
proposed link and variance function, applies an ad hoc optimiza-
tion criterion. It corresponds to employing a weighted version of a
normal likelihood for data that is clearly not normally distributed.
More concerning is that it ignores the evident dependence be-
( ) ( )
tween the sites, or Z's, for example, between Z s, s′ and Z s, s′′ .
• Second, the choice of a binomial variance function seems to be
( )
motivated by thinking about Z si , sj arising as some sort of pro-
portion associated with a sum of independent and identically
distributed (i.i.d.) Bernoulli trials. Even if the ecological dissimi-
larity measure is based on presence/absence data, there are no
such trials to imagine such a variance function. When applied to
abundance data, for example, per cent plant cover in a sample site,
such a variance function is clearly inappropriate. Furthermore,
GDM assumes that variance in dissimilarity behaves proportion-
ally to 𝜇(1 − 𝜇), equivalently in terms of the transformed ecologi-
cal distance, 𝜂. We explore whether this assumption is appropriate
below. We note that Ferrari and Cribari-Neto (2004) and Ferrier
et al. (2007) suggest that other variance functions associated with
[ ]
distributions on 0, 1 could be investigated. This would not rem-
edy the concern regarding the absence of a likelihood.
• Third, bootstrapping uncertainty is tenuous, even if the pro-
posed optimization criterion were suitable, because it assumes
( ) ( )
independent observations and clearly Z si , sj and Z si , sk are not
independent. However, such dependence across sites can be en-
visaged through structured spatial dependence.
• Fourth, the GDM ignores the need for a point mass at 1, that is,
the one-inflation problem. In our species-level dataset below,
essentially half of the dissimilarities are equal to 1. These pairs
cannot be ignored in the model fitting and modelling them to be
less than 1 with probability 1 denies the reality of the dissimilarity
process realization over  × . One might suggest deleting the
perfect dissimilarities. This can certainly introduce sampling bias.
Furthermore, apart from losing a potentially large amount of in-
formative data (≈ 50 % in our GCFR family-level data), it is unclear
2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
WHITE et al.
how to do this. If one deletes a Zij because it is exactly 1, in prin-
ciple should one delete site i , that is, all Zij′ , j′ ≠ j? Similarly, should
one delete site j all other Zi′ j , i′ ≠ i? With a high incidence of 1s,
if one implemented this over all of the 1s, likely little data would
remain.
• Finally, the modelling is not generative and could not have pro-
duced the dissimilarities we observe. That is, the implicit likeli-
hood being optimized is inappropriate and is not a likelihood for
the data. Given the strong interest in illuminating the complex
processes of biodiversity, there is a need for models that extend
beyond a patchwork of statistical pieces. We would also note that
adoption of such regression modelling necessitates investigation
of model adequacy and model comparison, not currently consid-
ered with the GDM.
1.2 | A proposed remedy: Generative spatial
generalized dissimilarity mixed modelling
Given the criticisms listed in the previous section, we propose an
alternative hierarchical Bayesian modelling framework to remedy
these criticisms. We refer to our proposed model as a generative
spatial generalized dissimilarity mixed modelling (spGDMM). In this
paper, we also use spGDMM to represent spatial generalized dis-
similarity mixed model. The main aspects of our contribution are:
(i) for study region, , we offer fully spatial modelling for the
( ) ( )
dissimilarity Z s, s′ between s and s′ with s, s� ∈  × . That
is, conceptually, the latter is the space over which pairwise
dissimilarity exists. This requires introduction of novel spatial
random effects modelling, with attractive interpretation, added
to the mean regression term. Furthermore, these random ef-
fects enable us to capture the evident probabilistic dependence
( ) ( )
between, for example, Z s, s′ and Z s, s′′ . Additionally, we
demonstrate the need for a flexible heterogeneity of variance
( )
specification for Z s, s′ ;
(ii) our approach enables spatial interpolation of dissimilarity. In
principle, this can be done with the GDM approach. However,
prediction incorporating spatial dependence performs better, as
we demonstrate through kriging, holding out pairs of sites. In
this regard, we offer novel out-of-sample model validation and
comparison;
(iii) we offer a formal stochastic treatment for the incidence of 1s,
employing right truncation to provide a point mass at 1. The
point mass is induced through transformation of a latent dissim-
ilarity; and
(iv) we do all the above through specification of an explicit hierar-
chical model. Such modelling, fitted within a Bayesian frame-
work, enables us to obtain full inference and uncertainty.
Furthermore, such modelling is generative, and thus equiv-
alently, coherent, that is, it prescribes a probabilistic specifi-
cation which can generate the dissimilarity data we observe.
Importantly, it can generate perfect dissimilarities.

WHITE et al.
2 | M ATE R I A L S A N D M E TH O DS
2.1 | Data and dissimilarity
We fit the spGDMM to three datasets. To anchor our analysis, two
of these datasets are prominent and accessible examples that are
well described in the GDM literature. The first and primary dataset
we analyse is from van der Merwe et al. (2008a, 2008b) consisting
of per cent cover data of all plant species at 413 sites in the Hantam–
Tanqua–Rogeveld subregion of South Africa's Greater Cape Floristic
Region (GCFR; Figure 1). Given that these data have not been de-
scribed in the context of GDMs, we describe the ecological aspects
of the data in Supporting Information A. Since the level of species
turnover is particularly high, we also model the rates of turnover at
the family level. The sites contain 288 species, 144 genera and 52
families. For each site s, we observe a vector of per cent cover for
each taxonomic group (species or family) Y(s).
n ⎛ ⎞ We selected a set of seven explanatory variables for the GCFR
⎜ ⎟ = 85,078 ( )
For 413 sites, we have ⎜⎝ 2 ⎟⎠ pairwise dissimilarities Z s, s′ ,
observed in . Specifically, we use Bray–Curtis (BC) dissimilarity on
the available per cent cover data. Because per cent cover is a contin-
uous variable, the BC dissimilarity is
∑ � �
� � j ∣ Yj (s) − Yj s� ∣
Z s, s �
= ∑
j ∣ Yj (s) + Yj (s� ) ∣
( ) ( ) ( )
For Z s, s� = 0, Yj (s) = Yj s� for all j. For Z s, s� = 1, locations s and s′
must have no species (or families) in common. We note that the Panama
and southwest Australia data have a low proportion of locations with
F I G U R E 1 Location of sites in the Greater Cape Floristic
Region in South Africa overlaid a map of biome boundaries. Biome
boundaries derived from (South African National Biodiversity
Institute, 2006).
|
2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
217
complete dissimilarity, while this is quite prevalent in the South African
dataset, particularly at the species level.
The computed dissimilarity depends on the taxonomic scale
considered. If computing the dissimilarity at species scale, then
( )
Z s, s′ arises as a sum over 288 terms. At family scale, we sum over
52 terms. In this manuscript, we focus our discussion on dissimilar-
ities calculated at family level; however, we also include some re-
sults for a species-level analysis and present more detailed results in
Supporting Information E.
We plot the family- and species-level dissimilarities against the
spatial distance between sites in Figure 2. In addition, we plot mean
dissimilarity and the proportion of dissimilarities equal to 1 as a func-
tion of distance. At family scale, 4.6% of the observed dissimilarities
are exactly 1. This increases to 49% at the species scale, frequently
occurring across all spatial distances. In fact, mean dissimilarity is
very large even at short distances. An appropriate generative model
for data like this must include a point mass at 1.
data that captured a range of climatic, topographic and edaphic
features that could likely drive turnover in taxa. These variables
are described in further detail in Supporting Information A. For the
Panama and southwest Australia data, we use explanatory variables
that were provided with datasets described by Ferrier et al. (2007)
and Fitzpatrick et al. (2013) respectively.
. (2)
The second dataset consists of 39 survey sites of 225 rainforest
tree species from Panama's Barro Colorado Island (BCI), initially de-
scribed by Condit et al. (2002) and presented in the GDM context
by Ferrier et al. (2007). We use only 39 of the 50 sites because 11
are not geocoded. The third dataset consists of occurrence data for
856 plant species across 94 locations in southwest Australia. This
is the example dataset provided in the ‘gdm’ R Package (Fitzpatrick
et al., 2022a) which is a subset of the data described by Fitzpatrick
et al. (2013).
3 | O U R M O D E LLI N G A PPROAC H
3.1 | Model specifications
( )
We model Z si , sj , the dissimilarity between sites si and sj, explicitly
( ) ( )
through Z si , sj = min 1, eV (si ,sj ) , where
( ) ( ( ) ( ) ( ))
V si , sj ∼ N 𝜇 si , sj + 𝜂 si , sj , 𝜎 2 si , sj . (3)
So, we immediately obtain a point mass at 1 for the distribu-
( ) ( ) ( )
tion of Z si , sj whenever V si , sj ≥ 0, and Z si , sj ∈ (0, 1) when
( )
V si , sj < 0 . That is, we adopt a version of the usual Tobit regres-
( )
sion setting, introducing V si , sj as a ‘latent dissimilarity’ on R1.
Whenever the latent dissimilarity becomes large enough (≥ 0)
the observed dissimilarity becomes 1. Unlike many inflation ap-
proaches, like hurdle model or 0- and one-inflated beta models
(Ospina & Ferrari, 2012), the point mass is driven solely by the
dissimilarity model rather than a logistic regression model for each
 |

2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
218 WHITE et al.

1.00 1.00 F I G U R E 2 Two-dimensional histogram

on the Bray–Curtis dissimilarities plotted
against distance between sites calculated
at (Left) family scale and (Right) species
Bray−Curtis dissimilarity

Bray−Curtis dissimilarity
0.75 0.75
scale for data within the Greater Cape
Count
400
Count
4000
Floristic Region. The cyan line marks the
0.50
300
0.50
3000
mean BC dissimilarity over 25 km bins, and
200 2000

100 1000 the green line plots the proportion of BC

dissimilarities equal to 1 over 25 km bins.
0.25 0.25

0.00 0.00
0 100 200 300 0 100 200 300
Distance (km) Distance (km)

point mass. As a result, our model provides coherence for the clear
one-inflation present in observed BC dissimilarities. An alternative
link function that would allow both 0- and one-inflation, if needed,
is mentioned in Supporting Information C.1.
( )
So, our modelling effort is to consider specifications for 𝜇 si , sj ,
( ) ( )
𝜂 si , sj and 𝜎 2 si , sj . Our primary contributions come through our
( ) ( ) ( )
specifications of 𝜂 si , sj and 𝜎 2 si , sj . In particular, for 𝜇 si , sj we
consider the form
� � � � � � � �� � � ��
𝜇 si , sj = 𝛽 0 + 𝛽 1 h ‖ si − sj ‖ + 𝛼 k ‖ fk Xk si − fk Xk sj ‖ , (4)
k
analogous to expression (1). The parameter 𝛽 0 represents the base-
( )
line log-dissimilarity. That is, it determines the mean of V si , sj when
si = sj (see below and Supporting Information B1 for further discussion
regarding 𝛽 0). Here, h( ⋅ ) will be an increasing function, arguing that,
with 𝛽 1 > 0, transformed dissimilarity increases with distance between
sites. Here, the XK's are covariates with fk ( ⋅ ) increasing, providing the
‘warping’ function for covariate Xk.
As in Ferrier et al. (2007), we adopt cubic I-spline basis func-
tions to specify h( ⋅ ) and fk ( ⋅ ) (Ramsay, 1988), each with two inte-
rior knots at the 33% and 67% of the predictor. However, we use
a reparametrization of the I-spline coefficients so that the warping
[ ]
functions h and fk map to 0, 1 for all k. This standardizes the predic-
tors, making all variables comparable through 𝛼 k and 𝛽 1. When inter-
preting our model output, 𝛽 1 and the 𝛼 k parameters become variable
∑5
importance parameters. Specifically, we express h(x) = j=1 𝛽 h,j Ij (x)
∑5 ∑
and fk (x) = j=1 𝛽 fk ,j Ij (x), where Ij (x) are I-spline bases, j 𝛽 h,j = 1,
∑
j 𝛽 fk ,j = 1, and 𝛽 h,j , 𝛽 fk ,j > 0. Together, these constraints make h( ⋅ ) and
[ ]
fk ( ⋅ ) monotone increasing and bounded between 0, 1 . Although our
( )
specification of 𝜇 si , sj is analogous to that which is often proposed
for GDM's (see, e.g. Ferrier et al., 2007), the variable importance pa-
rameters add interpretability to the GDM framework. In sufficiently
rich datasets, h and/or fk could be spatially varying and estimated by
combining approaches in White et al. (2021, 2022).
( )
The role of 𝜂 si , sj is twofold. First, as in usual spatial model-
ling, we are adding a spatial random effect to provide adjustment to
the mean, to potentially capture the difference effects of unmea-
( )
sured variables. That is, as we specify 𝜂 s, s’ , it directly takes the
form of a non-negative difference in a latent covariate and enters
( )
the expression for V si , sj as a covariate would. In a different view,
it provides pairwise site adjustment to the global intercept 𝛽 0. It is
( )
clearly different from h si , sj which is a fixed effect as a function of
distance between sites. However, it is not a usual Gaussian process
(GP) adjustment in the ‘local’ sense since it is a function on R2 × R2. In
fact, we consider three choices for 𝜂 (and employ model comparison
below):
( )
• 𝜂 s, s� = 0, no spatial random effect
( �) ( ( ))2
• 𝜂 s, s = 𝜓(s) − 𝜓 s� , the squared difference between nor-
mals, suggesting a chi-square type of process
( �) ( )
• 𝜂 s, s = ∣ 𝜓(s) − 𝜓 s� ∣, the absolute difference between nor-
mals, suggesting a folded (or half) normal type of process
( )
Continuing, the 𝜂 s, s′ process with two arguments, is more
challenging than customary spatial random effects with a single
spatial argument. It provides spatial random effects over two spa-
tial locations and is not a function of the distance between the two
locations. The interpretation as a difference, squared or absolute,
( )
between a Gaussian process realization 𝜓(s) and 𝜓 s′ , in terms of
( ′)
adjusting the dissimilarity on the V s, s scale is intuitively clear. As
an adjustment, capturing potentially unmeasured or unobserved
predictors, it must be positive; it can only increase expected dis-
similarity as with the fixed effects in the mean. In different words,
since a dissimilarity is a function of two spatial arguments, so must
a spatial random effect in the mean (on a transformed scale). As an
adjustment, presumably, the closer the spatial locations, the smaller
the expected adjustment. However, for a pair of locations at a given
distance apart, this adjustment need not be the same as we move
around the study region. The Gaussian process and the ‘difference’
process that it induces enable this.
( )
For the second and third specifications above, 𝜂 s, s′ , as a func-
tion of a GP, is a realization of a stochastic process. This provides the
second role for the 𝜂's. They create expected dependence between the
V's and, hence, the Z's. In fact, using the second and third specifica-
( )
tions, we can explicitly calculate the covariance between V s1 , s2 and
( ) ( ) ( )
V s3 , s4 and, further, between Z s1 , s2 and Z s3 , s4 (see Supporting
Information C.2). No dependence is introduced in the absence of the 𝜂's.
Furthermore, the V's, hence the Z's are conditionally independent given

WHITE et al.
the 𝜂's, enabling us to write the likelihood over the Z's as a product form
which is convenient for model fitting. In Supporting Information C.2,
we digress technically to briefly consider properties arising under the
( )
foregoing specification of the random effect, 𝜂 s, s′ in the model for
( ) ( ) ( ( ))
Z s, s′ . We remark that, with 𝜂 s, s� = g 𝜓(s) − 𝜓 s� , 𝜂 is not a sta-
tionary function.
( )
We will see in Section 4 that the choice of 𝜂 s, s′ depends on
the taxonomic scale at which we calculate the BC dissimilarity.
We prefer the squared form at the species level but the absolute
( )
form at the family level. Furthermore, 𝜂 si , sj introduces the dif-
ference between a Gaussian process realization at si and at sj. So,
𝜂(s, s) = 0 with probability 1. We discuss this point in Supporting
Information C.2.
( )
We also consider three choices for 𝜎2 si , sj to capture variance
patterns suggested by Supporting Information A.2:
• 𝜎 2 constant, the homogeneous variance case
� � ��
• log 𝜎 2 s, s� = g( ‖ s − s ‖ ), with g a random function, giving a het-
erogeneous variance as a function of distance. In this case, we
let g( ⋅ ) be a cubic polynomial in distance. There is an intuitive ar-
gument that the variance of the difference should increase as a
function of distance (in the spirit of a variogram). However, this in-
tuition is contradicted by the patterns in Figure A.1 of Supporting
Information A. Thus, we let g( ⋅ ) be unconstrained.
( ( )) ( ( ))
• Finally, we consider log 𝜎 2 s, s� = g 𝜇 s, s� where now g is a
( ′)
function of 𝜇 s, s . Again, g( ⋅ ) is estimated, in the form of a cubic
polynomial. In preliminary modelling, we found that this formula-
tion is only estimated effectively with large datasets, so we only
present it for the South Africa data.
Ultimately, we choose the final model specification through
cross-validation (Section 3.2).
In summary, our models are more complex than the customary
GDM. However, in order to remedy our concerns with the latter, our
extension has only added the novel spatial random effects and more
flexible variance structure. Our proposed spGDMM can be used for cus-
tomary regression inference and for prediction, as in Ferrier et al. (2020)
and Hoskins et al. (2020). With prediction as a primary target, our model
selection criteria are motivated by performance in the data space,
that is, in out-of-sample predictive performance. Criteria such as AIC,
BIC or WAIC judge performance in parameter space. Ultimately, we
choose across a set of model specifications through cross-validation
(Section 3.2). We do not employ leave-one-out (loo) validation; it is a
‘simple’ version of the cross-validation that we do. We learn more about
model performance if we hold out a larger set and replicate.
Under these specifications, we can calculate the expected dis-
( ( )) ( ( )) ( )
similarity, E Z s, s′ and var Z s, s′ given 𝜂 s, s′ . For the mean, we
obtain
( ( ) ( ))
( ( � ) ( � )) 𝜇 s, s� + 𝜂 s, s�
E Z s, s | 𝜂 s, s = Φ + ( ’)
𝜎(s, s� )
( ( �) ( �)
𝜇 s, s + 𝜂 s, s
e ( 𝜇 (s,s� )+𝜂 (s,s� ))+𝜎 2 (s,s� )∕2
Φ − − 𝜎 s, s
𝜎(s, s� )
|
2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
219
We defer this calculation to Supporting Information C.1 where we also
( ( ) ( ))
show the behaviour of E Z s, s’ | 𝜂 s, s’ . The calculation to obtain cov
( ( ) ( ))
Z s1 , s2 , Z s3 , s4 requires the bivariate normal cdf and becomes too
messy to be useful.
We use weakly informative prior distributions for all model
parameters. To fit the model we use Markov chain Monte Carlo
(MCMC) methods to sample from the posterior distribution 𝜋(𝜽| Z) of
all model parameters 𝜽 conditioned on all dissimilarities Z. Because
the posterior conditional distribution of 𝜎 2𝜓 is an inverse gamma dis-
tribution, we carry out a Gibbs update for this parameter. For further
details regarding priors, model fitting and prediction estimation see
Supporting Information B.1. Code and data are provided at https://​
zenodo.​org/​recor​ds/​10091442 (White, 2023).
3.2 | Model comparison
To assess the performance of spGDMM, model comparison is accom-
plished through 10-fold cross-validation on all three datasets. To do
the cross-validation, we randomly distribute all sites into 10 groups of
nearly equal size, and, in each stage of the cross-validation, we hold out
the 10% of sites associated with each partition and all dissimilarities
associated with those sites. After fitting the model to dissimilarities
associated with the training subset of sites, we predict the hold-out
dissimilarities. We repeat this procedure 10 times so that each site
in our dataset is held out exactly once. Because each dissimilarity is
associated with two sites, every dissimilarity is held out as test data
twice. We average predictive performance across the 10 experiments
using the criteria discussed below.
To compare models, we primarily use the (continuous) ranked
probability score (see Brown, 1974; Matheson & Winkler, 1976, for
early discussion), which we abbreviate as CRPS, because it is a strictly
proper scoring rule (Gneiting & Raftery, 2007). Although we use the
abbreviation CRPS, we emphasize that we are working with a mixture
of continuous values and a point mass at 1 (see Tang et al., 2023, for
similar discussion). Thus, strictly, this is not a continuous ranked prob-
ability score. In practice, however, we estimate the CRPS using the
empirical CDF of the predictions, where each prediction is associated
with each posterior sample from our MCMC model fitting (Krüger
et al., 2021). For ease of comparison with the GCFR data, we divide
all CRPS values by the smallest CRPS to give ‘relative CRPS’, which we
abbreviate as rCRPS. In addition to CRPS, we offer root mean squared
error (RMSE) and mean absolute error (MAE) as out-of-sample pre-
dictive criteria because they allow us to compare our models to those
proposed by Ferrier et al. (2007).
For the GCFR data, we also include a summary of how well
the model is capturing the exact 1s in the data. Specifically,
we calculate the proportion of 1s predicted correctly (PPC) in
the data using the posterior median of predictions. If we let
( )
Z̃ s, s� be the posterior predictive median for an unobserved
Z s, s and n1 be the number of ones in the test dataset, then
)
( �) (5) ∑ ∑ � � � � � �
. PPC = n1 i j 1 Z si , sj = 1, Z̃ si , sj = 1 , for all sites i in the
1
test set, while j sums over all sites. This PPC criterion enables
 |
220
examination of how well the model predicts exact 1s. The stan-
dard GDM cannot predict exact 1s, so it always has a PPC of 0.
Using the model comparison approach in Section 3.2, we com-
( ) ( )
pare all combinations of 𝜂 s, s′ and 𝜎 2 s, s′ discussed in Section 3
using CRPS, RMSE and MAE. In addition, using the same 10-fold
cross-validation approach, we fit the Ferrier et al. (2007) GDM
model implemented in R (Fitzpatrick et al., 2022a), employing the
same number of spline basis functions as we use. However, be-
cause the Ferrier et al. (2007) fitting does not provide predictive
distributions, we only compute RMSE and MAE. We also include
a naive model that predicts all dissimilarities to be the sample
mean of dissimilarities in the training set. For the family- and spe-
cies-level analyses of GCFR, as well as the Panama and Australia
data, we present the results of this comparison in Table 1.
4 | R E S U LT S
4.1 | Model comparison results
In comparison with the naive model (scalar mean only), for the fam-
ily-level analysis of the Greater Cape Floristic Region (GCFR), the
Ferrier model improves by about 7% and 8% in terms of RMSE and
MAE respectively (Table 1). Under our specifications, all but our
model 3 performed better than the Ferrier model in terms of RMSE
and MAE. For the family-level dissimilarity, two of our three models
without spatial random effects are marginally better in prediction
than the Ferrier et al. (2007) model. The models with spatial random
( )
effects 𝜂 s, s′ are much better in prediction than those without spa-
( )
tial random effects. The models using the 𝜒 2 specification of 𝜂 s, s′
( �)
were between 7 and 10% better than those where 𝜂 s, s = 0 , de-
( )
pending on the specification of 𝜎 2 s, s’ . The models using the folded
( )
normal specification of 𝜂 s, s′ were between 11% and 14% better
( �)
than those where 𝜂 s, s = 0, depending on the specification of
( )
𝜎 2 s, s′ .
For the GCFR data, the Ferrier model was 14.2% and 17.1% worse
than our best model in terms of RMSE and MAE respectively. Thus,
at family level, our modelling offers a consequential improvement
relative to the Ferrier model. Using only RMSE and MAE, the spa-
tial random effects models provide the greatest improvement. More
dramatically, our models can predict ones exactly, so all our models
show some capacity in terms of PPC, while the Ferrier model offers
none. Interestingly, at family level, our models cannot predict zeros
with any accuracy unless they have spatial random effects, suggest-
ing that the covariates and distance are insufficient to explain com-
plete assemblage similarity. Our best models correctly predict 46%
of the observed 1s exactly using the posterior predictive median. In
terms of CRPS, the best model was Model 6, which uses the folded
( )
normal specification of 𝜂 s, s′ and variance function that is a func-
( ′)
tion of 𝜇 s, s . Thus, we use this model to present our results. Model
5 was competitive with Model 6 in CRPS and outperformed Model
6 in terms of RMSE and MAE. However, we ultimately use CRPS for
model selection.
2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
WHITE et al.
For the species-level analysis, the Ferrier model improves on the
naive model by 7% and 11% in terms of RMSE and MAE respec-
tively. Our best model improves upon the Ferrier model by 2.5% and
5.5% using RMSE and MAE respectively. Greater improvement over
the GDM model occurs at the family level because the dissimilari-
ties are smaller (mean dissimilarity of roughly 0.6) relative to those
at the species level (mean dissimilarity of 0.9), allowing more scale
to improve. In different words, the improvement, relatively, is more
substantial than it appears. This is apart from the empirical fact that
roughly 50% of species-level dissimilarities are 1, mandating the
need to specify a point mass at 1 in the modelling to enable exact
prediction of a 1. Again, the GDM model cannot predict a dissim-
ilarity of exactly 1; thus, its PPC is 0. This point is emphasized by
the results in Table 1, where our best model (in terms of predict-
ing zeros correctly) is able to correctly predict 62% of the exact 1s,
and predicted approximately 45% of the dissimilarities to be exactly
1. When analysing dissimilarities at species scale, the best model
in terms of CRPS was Model 9 which uses the 𝜒 2 specification for
( ) ( )
𝜂 s, s′ and variance as a function of 𝜇 s, s′ . This reveals that differ-
ent taxonomic scales can influence the selected model.
Compared to the best model for the BCI data, the Ferrier model is
14% and 16% worse in prediction using RMSE and MAE. The Ferrier
model is better than the non-spatial models allowing one-inflation.
Models with spatial random effects consistently outperform the
Ferrier model, highlighting the significance of incorporating the spa-
tial random effects for improved prediction accuracy. The Australia
data serves as an example where our framework demonstrates mar-
ginal benefit. Compared to our best model, the Ferrier model shows
only a 1% increase in prediction error measured by RMSE and MAE.
Surprisingly, the Ferrier model outperforms all but one of the sp-
GDMM models in terms of RMSE and MAE. We speculate that this
can be attributed to the presence of very low levels of one-inflation
and a relatively weak spatial residual structure in the dissimilarities.
4.2 | Inference
4.2.1 | Variable importance and response curves
Because we constrain the environmental warping functions fk ( ⋅ ) and
distance warping function h( ⋅ ) to be monotone increasing from 0 to
1, we can compare the relative importance of each variable through
the variable importance parameters: 𝛽 1 and 𝛼 k. We emphasize that
these parameters enter the model through the shape given by fk. We
plot the posterior means and 90% credible intervals for the variable
importance parameters in Figure 3 for the GCFR, BCI and south-
west Australia data. Inferential results of the GCFR data focus on
our family-level analysis.
Four of the seven environmental variables in the GCFR data have
posterior mean variable importances greater than 0.1: annual pre-
cipitation, heat load index, elevation and soil nitrogen (listed in order
of importance). The BCI data had two of three variables with impor-
tances greater than 0.1 (distance and elevation), while the southwest
 |

2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
WHITE et al. 221

TA B L E 1 Cross-validation model comparison results for (Top) the family-level analysis of GCFR dissimilarities, (Middle) the species-level
analysis of GCFR dissimilarity and (Bottom) BCI and Australia dissimilarities. Best performances are bolded. We do not include models with
( ( ))
g 𝜇 s, s′ in the BCI and Australia data due to small sample size. Model numbering is consistent across Tables.

Model rCRPS CRPS RMSE MAE PPC

( ) ( )
𝜼 s, s′ 𝝈 2 s, s′

Naive — — — — 0.2075 0.1711 0.0000

Ferrier — — — — 0.1922 0.1569 0.0000
1 0 𝜎2 1.1372 0.1104 0.1916 0.1566 0.0184
( )
2 0 g ∥ s − s� ∥ 1.1389 0.1106 0.1919 0.1568 0.0212
( ( ))
3 0 g 𝜇 s, s′ 1.1432 0.1110 0.1926 0.1573 0.0060
( )
4 ∣ 𝜓(s) − 𝜓 s� ∣ 𝜎 2 1.0115 0.0982 0.1701 0.1350 0.4500
( ) ( )
5 ∣ 𝜓(s) − 𝜓 s� ∣ g ∥s−s ∥ � 1.0007 0.0972 0.1683 0.1340 0.4605
( ) ( ( ))
6 ∣ 𝜓(s) − 𝜓 s� ∣ g 𝜇 s, s′ 1.0000 0.0971 0.1698 0.1342 0.3467
7 ( ( ))2 1.0464 0.1016 0.1757 0.1401 0.4318
𝜓(s) − 𝜓 s� 𝜎2
( ( ))2 ( )
8 𝜓(s) − 𝜓 s� g ∥ s − s� ∥ 1.0508 0.1020 0.1763 0.1413 0.3740
( ( ))2 ( ( ))
9 𝜓(s) − 𝜓 s� g 𝜇 s, s′ 1.0760 0.1045 0.1823 0.1454 0.3286

Model rCRPS CRPS RMSE MAE PPC

( ) 2
( )
𝜼 s, s′ 𝝈 s, s ′

Naive — — — — 0.1028 0.0801 0.0000

Ferrier — — — — 0.0954 0.0714 0.0000
1 0 𝜎2 1.0499 0.0467 0.0962 0.0741 0.3179
( )
2 0 g ∥ s − s� ∥ 1.0474 0.0466 0.0962 0.0736 0.3663
( ( ))
3 0 g 𝜇 s, s′ 1.0484 0.0467 0.0959 0.0720 0.5029
( )
4 ∣ 𝜓(s) − 𝜓 s� ∣ 𝜎 2 1.0079 0.0449 0.0934 0.0681 0.6198
( ) ( )
5 ∣ 𝜓(s) − 𝜓 s� ∣ g ∥s−s ∥ � 1.0128 0.0451 0.0938 0.0684 0.6141
( ) ( ( ))
6 ∣ 𝜓(s) − 𝜓 s� ∣ g 𝜇 s, s′ 1.0097 0.0450 0.0938 0.0669 0.4316
7 ( ( ))2 2 1.0099 0.0450 0.0936 0.0699 0.4830
𝜓(s) − 𝜓 s� 𝜎
( ( ))2 ( )
8 𝜓(s) − 𝜓 s� g ∥s−s ∥ � 1.0034 0.0447 0.0933 0.0690 0.5484
( ( ))2 ( ( ))
9 𝜓(s) − 𝜓 s� g 𝜇 s, s′ 1.0000 0.0445 0.0930 0.0675 0.4746

BCI dataset Australia dataset

Model CRPS RMSE MAE CRPS RMSE MAE

( ) ( )
𝜼 s, s’ 𝝈2 s, s′

Naive — — — 0.1269 0.1036 — 0.1574 0.1307

Ferrier — — — 0.0934 0.0716 — 0.0737 0.0549
1 0 𝜎2 0.0527 0.0954 0.0779 0.0439 0.0790 0.0595
( )
2 0 g ∥ s − s’ ∥ 0.0511 0.0937 0.0734 0.0435 0.0805 0.0608
( )
4 ∣ 𝜓(s) − 𝜓 s� ∣ 𝜎 2 0.0490 0.0878 0.0690 0.0473 0.0840 0.0629
( ) ( )
5 ∣ 𝜓(s) − 𝜓 s� ∣ g ∥ s − s’ ∥ 0.0479 0.0879 0.0654 0.0454 0.0820 0.0626
7 ( ( ))2 2 0.0472 0.0856 0.0658 0.0414 0.0731 0.0545
𝜓(s) − 𝜓 s� 𝜎
( ( ))2 ( )
8 𝜓(s) − 𝜓 s� g ∥s−s ∥ � 0.0450 0.0821 0.0618 0.0407 0.0748 0.0556

Australian data had three of four variables with importances greater
than 0.1 (winter precipitation, distance and soil phosphorus).
The model suggests that annual precipitation (gmap) is the most
important driver of beta diversity in the South Africa data, holding
all other variables constant. Annual precipitation appears to be al-
most twice as important as the second most important environmen-
tal variable: heat load index (Theobald et al., 2015). Precipitation
was also found to be the most important variable for the southwest
Australian data, though the distance and phosphorus variables were
also quite close in importance. Holding all other variables constant,
both elevation and soil nitrogen are also important drivers of beta
diversity in the South Africa data.
To clarify how these environmental variables drive beta diversity
in the spGDMM, we plot the estimated 𝛼 k fk ( ⋅ ) for all covariates in
Figure 4. The warping functions, fk ( ⋅ ), are plotted without the vari-
able importance scaling in Supporting Information D. In these plots,
 |

2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
222 WHITE et al.

0.4 F I G U R E 3 90% credible intervals

on variable importance parameters for

Variable importance
0.3 (Top) Family-level analysis of GCFR data,
(Bottom-Left) Panama data and (Bottom-
0.2
Right) Australia Data.
0.1

0.0
Pre

Ra

Ele

He

Me

So

So

Dis
il

il N
in

an
va

ta
c

tL

Co
ipit

fal

nc
tio

itro
Te
oa
l

n
ati

e
n
Co

du
mp
d

g
on

en
n

ctiv
c.

ity
0.4
0.4

Variable importance
Variable importance

0.3
0.3

0.2 0.2

0.1 0.1

0.0 0.0
Ph

Te

Pre

Dis
Pre

Ele

Dis

m
os

tan
va

tan

cip
cip

pe
ph
tio

it

ce
ita

ce

rat

ati
oru
n
tio

on
re
s
n

we fix the scale of the y-axis so that the relative importance of these For the Panama data, the Ferrier model showed weak effects
variables is clear. In addition, we add the estimated warping curve (< 0.1 %) for precipitation on beta diversity while the spGDMM
using the Ferrier model. Our model for the warping is on the scale found none. The spGDMM found weak effects of elevation on beta
of the latent log-dissimilarity and the Ferrier model is on the scale diversity that increased between 200 and 600 m and tapered after
of 1 − e−𝜇. To allow comparison between the inference provided by 600 m. The Ferrier model found similar results, though at stronger
our model and the Ferrier GDM model, we multiply all estimated effect levels. Both models found that distance had strong effects for
curves from the Ferrier model by a common scaling factor so that beta diversity with the spGDMM finding a steep effect increasing
the highest point on any curve is equal to the highest point on the between 0 and 20 km while the Ferrier model showed a steadier in-
posterior mean curves. crease across the distance range.
Holding other covariates constant in the South Africa data, The spGDMM and Ferrier model results often overlapped in
annual average precipitation has almost no estimated impact on the Australia data. The most significant departure between the two
beta diversity until the average exceeds 300 mm according to models was for the distance variable with the Ferrier model finding
estimates from the spGDMM. Beyond 300 mm, annual precipi- a weak, but steadily increasing effect of distance on beta diversity.
tation has a very strong impact on beta diversity. This suggests The spGDMM found a strong effect that sharply increased between
that precipitation averages below 300 mm are effectively similar 0 and 150 km.
in terms of beta diversity. The Ferrier model found a similar result,
but showed an additional impact on beta diversity around 150 mm
of rainfall. The warping of elevation is approximately linear, with 4.3 | Spatial random effects
some tapering for elevations above 1300 m. The Ferrier model re-
sults behaved similarly but had a strong impact for elevation above We visualize the estimated spatial random effect surface in two ways
1300 m instead of tapering. From the estimated warping for heat in Figure 5. First, we plot the posterior mean of 𝜓(s). Second, we plot
( ) ( )
loads in Figure 4, heat loads less than 170 are effectively the same 𝜂 s, s� = ∣ 𝜓(s) − 𝜓 s� ∣, by fixing s and plotting the posterior mean
in terms of beta diversity. When heat loads exceed 170, there are as a function of s′. Every point s generates a surface that adjusts the
significant effects on beta diversity. The Ferrier model estimated dissimilarities at s′. These fixed s sites are located where we would ex-
that heat load had an effect at much smaller values, but tapered pect to find vegetation belonging to the Succulent Karoo and Fynbos
off around estimates of 190. Uniquely, the beta diversity driven by biomes respectively (See Figure 1). The scale of the differences in
( )
soil total nitrogen occurs at low values (< 0.1 %) for the spGDMM. 𝜂 s, s′ is large relative to the scale of the scaled warping functions in
Above 0.1% in soil total nitrogen, there is effectively no differ- Figure 4. This suggests that the spatial random effect contributes to
ence in beta diversity. The Ferrier model had similar dynamics but the mean dissimilarity more than the environmental covariates, even
showed a higher effect from soil nitrogen. We speculate that the when considering the additive effect of many environmental vari-
differences in results between the spGDMM and the Ferrier mode ables. As is discussed at length in the spatial confounding literature
arise in part from the inclusion of spatial random effects and the (see, e.g. Khan & Calder, 2022; Reich et al., 2006), it is likely that the
use of different link functions. spatial random effects diminish or alter the estimated effect of some
 |

2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
WHITE et al. 223

k fk(Annual precipiation (mm))

k fk(Rainfall concentration)
0.4

0.4

0.4

0.4
k fk(Elevation (m))

k fk(Heat load)
0.3

0.3

0.3

0.3
0.2

0.2

0.2

0.2
0.1

0.1

0.1

0.1
0.0

0.0

0.0

0.0
100 200 300 10 20 30 40 50 500 1000 1500 120 140 160 180 200 220 240
Annual precipiation (mm) Rainfall concentration Elevation (m) Heat load
0.4

0.4

0.4

0.4
k fk(Soil conductivity)
k fk(Mean temp (C))

k fk(Soil nitrogen)
0.3

0.3

0.3

0.3
f(Distance)
0.2

0.2

0.2

0.2
0.1

0.1

0.1

0.1
0.0

0.0

0.0

0.0
12 14 16 18 20 20 40 60 80 100 0.05 0.10 0.15 0.20 0.25 0.30 0 50 100 150 200 250 300
Mean temp (C) Soil conductivity Soil nitrogen Distance (km)
k fk(Precipitation (mm))
0.4

0.4

0.4
k fk(Eleveation (m))

f(Distance)
0.3

0.3

0.3
0.2

0.2

0.2
0.1

0.1

0.1
0.0

0.0

0.0

2000 2500 3000 3500 4000 0 200 400 600 800 0 20 40 60 80 100
Precipitation (mm) Eleveation (m) Distance (km)
k fk(Winter precipitation (mm))
0.5

0.5

0.5

0.5
k fk(Max temperature (C))
k fk(Soil phosphorus)
0.4

0.4

0.4

0.4
f(Distance)
0.3

0.3

0.3

0.3
0.2

0.2

0.2

0.2
0.1

0.1

0.1

0.1
0.0

0.0

0.0

0.0

100 200 300 400 500 500 1000 1500 26 28 30 32 34 36 100 300 500 700
Winter precipitation (mm) Soil phosphorus Max temperature (C) Distance (km)

F I G U R E 4 Product of variable importance parameter (𝛼 k or 𝛽 1) and warping function. Posterior mean in black, 90% credible interval in
grey, and scaled curves from Ferrier model in red. (Top/Top-Middle) all covariates for the family level analysis of the GCFR data; (Bottom-
Middle) precipitation, elevation and distance curves for Panama data; (Bottom) winter precipitation, soil phosphorus, max temperature and
distance for Australia data. Within a dataset, all curves are plotted on fixed y-scale.

of the environmental predictors. We note that much of the random become a standard tool for many ecologists (Mokany et al., 2022) be-
effect signal we observed in the posterior means likely corresponds cause of their capacity to handle the nonlinear relationship between
with biome transitions from Succulent Karoo to Fynbos biomes compositional dissimilarity and environmental distance as well as their
along the edge of the escarpment. accessibility in software implementation (Fitzpatrick et al., 2022b). While
the original GDM framework has advanced our understanding of beta
diversity patterns and what drives them, it does not offer a coherent
5 | DISCUSSION solution that could generate the data observed. In response, we have
proposed a generative spatial model that we refer to as the spGDMM.
Understanding and predicting turnover across landscapes is critical to We believe that the spGDMM approach is a useful step forward
biodiversity studies and conservation planning. GDMs have, perhaps, for explaining turnover in a rigorous manner. Using a suitable link
 |
224
−30.5 −30.5
−31.0 −31.0
Posterior
−31.5 Mean −31.5
1.0
lat
lat
0.5
0.0
−32.0 −0.5 −32.0
−1.0
−32.5 −32.5
−33.0 −33.0
19 20 21 19
lon
( )
F I G U R E 5 Posterior mean of (left) 𝜓(s) using the 𝜂 s, s� = ∣ 𝜓(s) − 𝜓 s� ∣ specification for the family-level analysis and (Centre-Right)
( �) ( �)
𝜂 s, s = ∣ 𝜓(s) − 𝜓 s ∣ for two fixed points indicated by points at s = (20.0, − 31.5), (19.6, − 32.3) respectively.
function (others are available, see Supporting Information C), we
have specified a model with a flexible spatially varying mean function
as well as spatially varying variances. Perhaps more importantly, we
have incorporated novel spatial random effects to capture depen-
dence between dissimilarities as well as to improve out-of-sample
prediction of dissimilarities. We have also implemented one-infla-
tion, acknowledging that, at the species level in the Greater Cape
Floristic Region (GCFR), essentially half of the observed dissimilar-
ities are 1.
We found that our spGDMM yielded consequential predictive
improvement over the GDM approach of Ferrier et al. (2007) par-
ticularly for the GCFR plant dataset. Our results confirm adequate
predictive capacity for other ecosystems when our models were
applied to the Barro Colorado Island (BCI) and southwest Australia
data (Section 4.1). In terms of inference, the model conclusions
were often similar though we note that the differences in results
between our models and the Ferrier model arise in part from the
inclusion of spatial random effects and the use of different link
functions. We highlight that our model is able to predict dissimi-
larities with a value of 1 (total dissimilarity) while the Ferrier model
cannot. We feel that this is a valuable contribution because many
biodiversity hotspots, for example, the GCFR, are characterized by
their large degree of species turnover (Latimer et al., 2005) which
in turn would lead to a high proportion of 1s even within small
spatial extents that are well sampled. This will also be the case in
broad-scale studies that examine biodiversity across regional to
global scales. Furthermore, given the time and resources needed
to survey an area in terms of its species, one can imagine a sce-
nario where limited samples within a diverse area can easily inflate
the proportions of 1s, creating a need for models that handle their
prevalence.
In terms of inferring what drives plant family turnover within the
GCFR, we found that mean annual precipitation, heat load index, el-
evation and soil nitrogen were the most important of the eight vari-
ables that we examined. Broadly, these results align with previous
efforts to examine turnover in the region. Factors such as climate,
topography and edaphic features have been highlighted in driving
turnover in taxonomic composition and subsequently turnover in bi-
omes (Mucina & Rutherford, 2006; Power et al., 2017). Out of all the
2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
WHITE et al.
−30.5
−31.0
Posterior Posterior
Mean −31.5 Mean
1.6
lat
0.9 1.2
0.6 0.8
0.3 −32.0 0.4
0.0 0.0
−32.5
−33.0
20 21 19 20 21
lon lon
( )
variables examined, we found that mean annual precipitation was the
most important in explaining beta diversity. This result is also echoed
in the southwest Australia data where the amount of winter rainfall
was the most important factor in driving plant species turnover in
the Mediterranean portion of the continent, matching the findings of
Fitzpatrick et al. (2013). Mean annual precipitation and heat load index
had relatively sharp thresholds with their relationship to beta diver-
sity. We hypothesize that the sharp increases of these two variables
are likely indications of turnover in biomes, particularly the transition
of the arid Succulent Karoo to fire-prone Fynbos biomes. The mean
annual precipitation for the Succulent Karoo is around 170 mm with
the wettest areas reaching levels of 300 mm (Mucina et al., 2006).
Strikingly, the threshold of 300 mm is also where our results for annual
precipitation start to strongly impact beta diversity. The threshold of
the heat load index is also likely the point where moisture availability
favours Succulent Karoo over Fynbos vegetation either through the
absence of fire or greater seed viability for succulent karoo vegetation
in drier areas (Rebelo et al., 2006).
The spatial random effects in our models play an important role,
contributing more to explain mean dissimilarity than our environ-
mental covariates. This makes a strong case for the need to include
spatial random effects in future dissimilarity modelling. Within our
data, we believe that the spatial random effects are capturing un-
measured local and regional factors that are likely related to biome
turnover. As seen in Figure 5, the two fixed points are roughly lo-
cated in an area of Succulent Karoo (left) and Fynbos (right). The
magnitudes of the random effect are lower where we would expect
the same biome of the fixed point and higher where we would ex-
pect a different biome.
There are several future applications that can be developed based
on the generative spatial models we describe. The incorporation of
spatial random effects can produce a number of hypotheses regard-
ing spatial patterns and processes that can subsequently be explored
and tested explicitly (Latimer et al., 2006, 2009). Future work could
include the investigation of the temporal dynamics of turnover lead-
( )
ing to a model that considers Z Yt1 (s), Yt2 (s) , that is, the dissimilarity
of a site between times t1 and t2. An even richer effort would con-
( ( ))
sider spatio-temporal turnover, Z Yt1 (s), Yt2 s� to better understand
change in biodiversity in the past and to project future changes. This

WHITE et al.
would enable assessment of within-site behaviour/variability versus
between-site behaviour/variability of Z. Another direction could con-
sider spatially varying coefficients in 𝜇 to enable the relationship to
be local rather than global. This will be novel but very challenging be-
cause, like the intercept adjustment, these coefficients will need two
arguments. A different path will consider biome-specific dissimilarity
when there are several biomes within the study region. Given the
complexity of biodiversity patterns and processes, the present mod-
elling of the spatial and environmental aspects of taxonomic turnover
only scratches the surface of what can be done in terms of under-
standing beta diversity.
AU T H O R C O N T R I B U T I O N S
Philip A. White and Alan E. Gelfand led the conceptualization,
development and implementation of the statistical analyses.
They also led the writing of the statistical review and critiques
of current generalized dissimilarity model approaches. Jasper A.
Slingsby, Henry A. Frye and John A. Silander led the writing pro-
cess for the ecological contextualization and interpretation of the
models. They also helped guide the conceptualization of the man-
uscript. All authors contributed critically to the drafts and gave
final approval for publication.
AC K N O​W L E D
​ G E ​M E N T S
We thank Matthew Aiello-Lammens, Douglas Euston-Brown,
Hayley Kilroy Mollmann, Cory Merow, Helga van der Merwe and
Adam Wilson for their contributions in the data collection and
curation. Special thanks to Cape Nature and the Northern Cape
Department of Environment and Nature Conservation for per-
mission for the collection of leaf spectra and traits. Data collec-
tion efforts were made possible by funding from National Science
Foundation grant DEB-1046328 to J.A. Silander. Additional sup-
port was provided by the University of Connecticut, a Future
Investigators in NASA Earth and Space Science and Technology
(FINESST) grant award (80NSSC20K1659) and a NASA BioSCape
Award (80NSSC22K1383) to H.A. Frye and J.A. Silander, a as well
as National Research Foundation grant awards (118593, 142438 and
150926) to J.A. Slingsby.
C O N FL I C T O F I N T E R E S T S TAT E M E N T
The authors state that there is no conflict of interest.
PEER REVIEW
The peer review history for this article is available at https://​w ww.​
webof​s cien​ce.​com/​a pi/​g atew​ay/​wos/​p eer-​review/​10.​1111/​2041-​
210X.​14259​.
DATA AVA I L A B I L I T Y S TAT E M E N T
The Barro Colorado Island and Southwest Australia datasets are ac-
cessible from sources cited in the main manuscript. Data from the
Greater Cape Floristic Region, as well as code for the models im-
plemented using NIMBLE (de Valpine et al., 2017) are provided at
https://​zenodo.​org/​recor​ds/​10091442 (White, 2023).
|
2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
225
ORCID
Philip A. White https://orcid.org/0000-0003-0907-9221
Henry A. Frye https://orcid.org/0000-0002-2066-5742
Jasper A. Slingsby https://orcid.org/0000-0003-1246-1181
John A. Silander Jr https://orcid.org/0000-0001-8535-4710
Alan E. Gelfand https://orcid.org/0000-0002-5671-9212
REFERENCES
Anderson, M. J., Crist, T. O., Chase, J. M., Vellend, M., Inouye, B. D.,
Freestone, A. L., Sanders, N. J., Cornell, H. V., Comita, L. S., &
Davies, K. F. (2011). Navigating the multiple meanings of β diver-
sity: A roadmap for the practicing ecologist. Ecology Letters, 14(1),
19–28.
Blasco-Moreno, A., Pérez-Casany, M., Puig, P., Morante, M., & Castells,
E. (2019). What does a zero mean? Understanding false, random
and structural zeros in ecology. Methods in Ecology and Evolution,
10(7), 949–959.
Brown, T. A. (1974). Admissible scoring systems for continuous distributions.
Technical Report P-5235. The Rand Corporation.
Condit, R., Pitman, N., Leigh, E. G., Chave, J., Terborgh, J., Foster, R. B.,
Núñez, P., Aguilar, S., Valencia, R., Villa, G., Muller-Landau, H. C.,
Losos, E., & Hubbell, S. P. (2002). Beta-diversity in tropical forest
trees. Science, 295(5555), 666–669.
de Valpine, P., Turek, D., Paciorek, C. J., Anderson-Bergman, C., Lang, D.
T., & Bodik, R. (2017). Programming with models: Writing statistical
algorithms for general model structures with NIMBLE. Journal of
Computational and Graphical Statistics, 26(2), 403–413.
Ferrari, S., & Cribari-Neto, F. (2004). Beta regression for modelling rates
and proportions. Journal of Applied Statistics, 31(7), 799–815.
Ferrier, S. (2002). Mapping spatial pattern in biodiversity for regional
conservation planning: Where to from here? Systematic Biology,
51(2), 331–363.
Ferrier, S., Harwood, T. D., Ware, C., & Hoskins, A. J. (2020). A globally
applicable indicator of the capacity of terrestrial ecosystems to re-
tain biological diversity under climate change: The bioclimatic eco-
system resilience index. Ecological Indicators, 117, 106554.
Ferrier, S., Manion, G., Elith, J., & Richardson, K. (2007). Using gener-
alized dissimilarity modelling to analyse and predict patterns of
beta diversity in regional biodiversity assessment. Diversity and
Distributions, 13(3), 252–264.
Ferrier, S., Powell, G. V., Richardson, K. S., Manion, G., Overton, J. M.,
Allnutt, T. F., Cameron, S. E., Mantle, K., Burgess, N. D., & Faith, D.
P. (2004). Mapping more of terrestrial biodiversity for global con-
servation assessment. Bioscience, 54(12), 1101–1109.
Fitzpatrick, M., Mokany, K., Manion, G., Nieto-Lugilde, D., & Ferrier, S.
(2022a). gdm: Generalized dissimilarity modeling.
Fitzpatrick, M., Mokany, K., Manion, G., Nieto-Lugilde, D., & Ferrier, S.
(2022b). gdm: Generalized dissimilarity modeling. R package version
1.5.0-9.1.
Fitzpatrick, M. C., Sanders, N. J., Normand, S., Svenning, J.-C., Ferrier,
S., Gove, A. D., & Dunn, R. R. (2013). Environmental and histori-
cal imprints on beta diversity: Insights from variation in rates of
species turnover along gradients. Proceedings of the Royal Society B:
Biological Sciences, 280(1768), 20131201.
Gneiting, T., & Raftery, A. E. (2007). Strictly proper scoring rules, predic-
tion, and estimation. Journal of the American Statistical Association,
102(477), 359–378.
Graham, C. H., & Fine, P. V. A. (2008). Phylogenetic beta diversity: Linking
ecological and evolutionary processes across space in time. Ecology
Letters, 11(12), 1265–1277.
Hoskins, A. J., Harwood, T. D., Ware, C., Williams, K. J., Perry, J. J., Ota,
N., Croft, J. R., Yeates, D. K., Jetz, W., Golebiewski, M., Purvis,
A., Robertson, T., & Ferrier, S. (2020). BILBI: Supporting global
 |
226
biodiversity assessment through high-resolution macroecological
modelling. Environmental Modelling & Software, 132, 104806.
Khan, K., & Calder, C. A. (2022). Restricted spatial regression meth-
ods: Implications for inference. Journal of the American Statistical
Association, 117(537), 482–494.
Krüger, F., Lerch, S., Thorarinsdottir, T., & Gneiting, T. (2021). Predictive
inference based on markov chain Monte Carlo output. International
Statistical Review, 89(2), 274–301.
Latimer, A. M., Banerjee, S., Sang, H., Jr., Mosher, E. S., & Silander, J. A., Jr.
(2009). Hierarchical models facilitate spatial analysis of large data
sets: A case study on invasive plant species in the northeastern
United States. Ecology Letters, 12(2), 144–154.
Latimer, A. M., Silander, J. A., & Cowling, R. M. (2005). Neutral ecological
theory reveals isolation and rapid speciation in a biodiversity hot
spot. Science, 309(5741), 1722–1725.
Latimer, A. M., Wu, S., Gelfand, A. E., & Silander, J. A., Jr. (2006). Building
statistical models to analyze species distributions. Ecological
Applications, 16(1), 33–50.
Legendre, P. (1993). Spatial autocorrelation: Trouble or new paradigm?
Ecology, 74(6), 1659–1673.
Manly, B. F. (1986). Randomization and regression methods for testing for
associations with geographical, environmental and biological distances
between populations. Researches on Population Ecology, 28, 201–218.
Matheson, J. E., & Winkler, R. L. (1976). Scoring rules for continuous
probability distributions. Management Science, 22(10), 1087–1096.
Mokany, K., Ware, C., Woolley, S. N. C., Ferrier, S., & Fitzpatrick, M. C. (2022).
A working guide to harnessing generalized dissimilarity modelling for
biodiversity analysis and conservation assessment. Global Ecology and
Biogeography: A Journal of Macroecology, 31(4), 802–821.
Mucina, L., Jürgens, N., le Roux, A., Rutherford, M. C., Schmiedel, U., Esler,
K. J., Powrie, L. W., Desmet, P. G., & Milton, S. J. (2006). Succulent
Karoo Biome. In The Vegetation of South Africa, Lesotho and Swaziland,
Strelitzia. South African National Biodiversity Institute.
Mucina, L., & Rutherford, M. C. (Eds.). (2006). The vegetation of South
Africa, Lesotho and Swaziland. Number 19 in Strelitzia. South African
National Biodiversity Institute. OCLC: ocn137259974.
Oksanen, J., & Tonteri, T. (1995). Rate of compositional turnover along
gradients and total gradient length. Journal of Vegetation Science,
6(6), 815–824.
Ospina, R., & Ferrari, S. L. (2012). A general class of zero-or-one inflated
beta regression models. Computational Statistics & Data Analysis,
56(6), 1609–1623.
Power, S. C., Anthony Verboom, G., Bond, W. J., & Cramer, M. D. (2017).
Environmental correlates of biome-level floristic turnover in South
Africa. Journal of Biogeography, 44(8), 1745–1757.
Prentice, I. C. (1977). Non-metric ordination methods in ecology. The
Journal of Ecology, 65, 85–94.
Ramsay, J. O. (1988). Monotone regression splines in action. Statistical
Science, 3(4), 425–441.
Rebelo, A. G., Boucher, C., Helme, N., Mucina, L., & Rutherford, M. C.
(2006). Fynbos Biome. In The vegetation of South Africa, Lesotho, and
Swaziland, Strelitzia. South African National Biodiversity Institute.
Reich, B. J., Hodges, J. S., & Zadnik, V. (2006). Effects of residual smooth-
ing on the posterior of the fixed effects in disease-mapping models.
Biometrics, 62(4), 1197–1206.
Schweiger, A. K., & Laliberté, E. (2022). Plant beta-diversity across bi-
omes captured by imaging spectroscopy. Nature Communications,
13(1), 2767.
2041210x, 2024, 1, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14259 by CAPES, Wiley Online Library on [11/01/2024]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
WHITE et al.
South African National Biodiversity Institute. (2006). The vegetation
map of South AfricaLesotho, and Swaziland.
Tang, B., Frye, H. A., Gelfand, A. E., & Silander, J. A. (2023). Zero-inflated
Beta distribution regression modeling. Journal of Agricultural,
Biological and Environmental Statistics, 28(1), 117–137.
Theobald, D. M., Harrison-Atlas, D., Monahan, W. B., & Albano, C. M.
(2015). Ecologically-relevant maps of landforms and physio-
graphic diversity for climate adaptation planning. PLoS One, 10(12),
e0143619.
van der Merwe, H., van Rooyen, M. W., & van Rooyen, N. (2008a).
Vegetation of the Hantam-Tanqua-Roggeveld subregion, South
Africa. Part 1: Fynbos biome related vegetation. Koedoe, 50(1),
61–71.
van der Merwe, H., van Rooyen, M. W., & van Rooyen, N. (2008b).
Vegetation of the Hantam-Tanqua-Roggeveld subregion, South
Africa Part 2: Succulent Karoo biome related vegetation. Koedoe,
50(1), 160–183.
White, P. A. (2023). Data and code from: Generative spatial generalized
dissimilarity mixed modeling (spGDMM): An enhanced approach to
modelling beta diversity. Zenodo https://​doi.​org/​10.​5281/​zenodo.​
10091441
White, P. A., Frye, H., Christensen, M. F., Gelfand, A. E., & Silander, J. A.
(2022). Spatial functional data modeling of plant reflectances. The
Annals of Applied Statistics, 16(3), 1919–1936.
White, P. A., Keeler, D. G., & Rupper, S. (2021). Hierarchical integrated
spatial process modeling of monotone west antarctic snow density
curves. The Annals of Applied Statistics, 15(2), 556–571.
Whittaker, R. H. (1960). Vegetation of the Siskiyou mountains, Oregon
and California. Ecological Monographs, 30(3), 279–338.
S U P P O R T I N G I N FO R M AT I O N
Additional supporting information can be found online in the
Supporting Information section at the end of this article.
Supporting Information S1. We carry out additional data
explanations and exploratory analyses in Section A. We introduce
prior distributions, model fitting details, and prediction methods
in Section B. In Section C, we present an alternative link function
and present distribution theory for the spatial random effects. In
Sections D and E, we show additional results for the South Africa
data at family- and species-level. In Section F, we display the spatial
random effect for the Barro Colorado Island and Southwest Australia
datasets.
How to cite this article: White, P. A., Frye, H. A., Slingsby, J. A.,
Silander, J. A. Jr, & Gelfand, A. E. (2024). Generative spatial
generalized dissimilarity mixed modelling (spGDMM): An
enhanced approach to modelling beta diversity. Methods in
Ecology and Evolution, 15, 214–226. https://doi.
org/10.1111/2041-210X.14259