vignettes/Composite_variables.Rmd
Composite_variables.RmdIn this vignette we explain how to use composite variables in trophic
SDM. These variables are useful especially in species-rich network,
where some predators might have so many preys that assuming that each of
them has a differential effect on predator distribution is not only a
problem, but might seem ecologically unjustified. Instead, we could
expect the richness or diversity of prey, or whether at least a prey is
available, to be important. Hence, we implemented the use of composite
variables, i.e., variables that summarize the information of a large
number of variables from the graph in a few summary variables. Examples
of composite variables are prey richness or diversity, or a binary
variable set to one if the number of preys is above a certain threshold.
These variables assume that all species have the same impact on the
predator. An alternative is to group species in the metaweb to represent
trophic groups that clump together species that feed on, or are eaten
by, the same type of species. We can then construct composite variables
(e.g., their richness) for each of those trophic groups to better
represent the variety of resources for species like generalist or top
predators.
In webSDM it is possible to define an extremely large set
of composite variables using the arguments sp.formula and
sp.partition. In general, sp.formula allows
the definition of the composite variables, while
sp.partition allow to define the groups of preys (or
predator) for which each composite variable is calculate. Hereafter we
don’t provide a complete analyses of a case-study using composite
variables, but rather focus on the description of how to implement them
in webSDM. Finally, we will see how to include an
interaction between preys and the environment.
sp.formula can be a right hand side formula including
richness (i.e. the sum of its preys) and any transformations of
richness. Notice that only “richness” is allowed for now. However, we
will see how this already allow to build an extremely large set of
composite variable. We start with a simple case where we model species
as a function of the richness of their prey, with a polynomial of degree
two.
m = trophicSDM(Y, X, G,
env.formula = "~ X_1 + X_1^2",
family = binomial(link = "logit"), penal = NULL,
sp.formula = "richness + I(richness^2)",
mode = "prey", method = "glm")
#> Formula was modified since it led to identical columns of the design matrix (e.g. Y_1 or Y_1^2 for binary data)Notice that for predators that feed on a single prey (with
presence-absence data), their richness and the square of their richness
is exactly the same variable. In this case, trophicSDM()
removes the redundant variable but prints a warning message. We can see
the formulas created by the argument $form.all of the
fitted model.
m$form.all
#> $Y1
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y2
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y3
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y5
#> [1] "y ~ X_1+I(Y1 + Y2 + Y3)+I(I(Y1 + Y2 + Y3)^2)"
#>
#> $Y4
#> [1] "y ~ X_1+I(Y3)"
#>
#> $Y6
#> [1] "y ~ X_1+I(Y3 + Y5)+I(I(Y3 + Y5)^2)"We now set as composite variable a dummy variable specifying whether
there is at least one available prey or not. To do so we define
sp.formula = "I(richness>0)".
m = trophicSDM(Y,X,G,
env.formula = "~ X_1 + X_1^2",
family = binomial(link = "logit"), penal = NULL,
sp.formula = "I(richness>0)",
mode = "prey", method = "glm")Which leads to the following formulas:
m$form.all
#> $Y1
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y2
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y3
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y5
#> [1] "y ~ X_1+I(I(Y1 + Y2 + Y3) > 0)"
#>
#> $Y4
#> [1] "y ~ X_1+I(I(Y3) > 0)"
#>
#> $Y6
#> [1] "y ~ X_1+I(I(Y3 + Y5) > 0)"A halfway between considering that each species has a differential
effect on the predator (i.e., no composite variable), or that every prey
has the same effect (i.e., modeling predator as a function of prey
richness), is to create group of species that we assume to have the same
effect on the predator. Then, we can model predator as a function of
composite variables calculated on each of these groups. To do so, we
rely on the argument sp.partition. This parameters has to
be a list, where each element contain the species of the given
group.
For example, we can put species Y1 and Y2 in the same group, species Y3
and Y4 are alone in their group and Y5 and Y6 to form another group.
Then, we can specify whatever sp.formula, for example
using richness (with a quadratic term).
m = trophicSDM(Y,X,G, "~ X_1 + X_1^2",
family = binomial(link = "logit"), penal = NULL,
sp.partition = sp.partition,
sp.formula = "richness + I(richness^2)",
mode = "prey", method = "glm")
#> Formula was modified since it led to identical columns of the design matrix (e.g. Y_1 or Y_1^2 for binary data)
#> Formula was modified since it led to identical columns of the design matrix (e.g. Y_1 or Y_1^2 for binary data)
#> Formula was modified since it led to identical columns of the design matrix (e.g. Y_1 or Y_1^2 for binary data)Which leads to the following formulas:
m$form.all
#> $Y1
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y2
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y3
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y5
#> [1] "y ~ X_1+I((Y1 + Y2))+I(I((Y1 + Y2)^2))+I((Y3))"
#>
#> $Y4
#> [1] "y ~ X_1+I((Y3))"
#>
#> $Y6
#> [1] "y ~ X_1+I((Y3))+I((Y5))"In case we want to specify a composite variable that cannot be
created from a function of richness, the user can specify directly the
list of the biotic formulas in the sp.formula argument.
Importantly, notice that in this case trophicSDM() will not
create a new formula from the argument G and will not check
that the user-defined formula actually derives from G
(i.e. that predator-prey interactions described in the formulas derive
from G). For example, we might want to quantify the effect of the prey
Y5 on the predator Y6 when the prey Y3 is not available. To do so, we
define for species Y6 an interaction term between species Y5 and one
minus Y3 (i.e. a dummy variable that takes the value of 1 when species
Y5 is present and Y3 is absent). To do so, we define
sp.formula as a list describing the biotic formula for each
species.
sp.formula = list(Y1 = "",
Y2 = "",
Y3 = "",
Y4 = "Y3",
Y5 = "Y1",
Y6 = "I(Y5*(1-Y3))")
m = trophicSDM(Y,X,G, "~ X_1 + X_1^2",
family = binomial(link = "logit"), penal = NULL,
sp.formula = sp.formula,
mode = "prey", method = "glm")
#> We don't check that G and the graph induced by the sp.formula specified by the user match, nor that the latter is a graph. Please be careful about their consistency.
m$form.all
#> $Y1
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y2
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y3
#> [1] "y ~ X_1 + X_1^2"
#>
#> $Y5
#> [1] "y ~ X_1+Y1"
#>
#> $Y4
#> [1] "y ~ X_1+Y3"
#>
#> $Y6
#> [1] "y ~ X_1+I(Y5 * (1 - Y3))"When computing the importance of variables using the function
computeVariableImportance, you should be careful with the
definition of groups. Indeed, the function computes the variable
importance of each group as the sum of the standardised regression
coefficients containing some variables from the groups. Therefore, if
species from different groups of variable are merged in the same
composite variable, computeVariableImportance will sum the
regression coefficient of the composite variable in different groups,
leading to wrong results. For example, if
sp.formula = "richness" and
sp.partition = NULL, you should put all species in the same
group in the argument groups.
m = trophicSDM(Y,X,G,
env.formula = "~ X_1 + X_1^2",
family = binomial(link = "logit"), penal = NULL,
sp.formula = "richness + I(richness^2)",
mode = "prey", method = "glm")
#> Formula was modified since it led to identical columns of the design matrix (e.g. Y_1 or Y_1^2 for binary data)
computeVariableImportance(m, groups = list("abiotic" = c("X_1", "X_2"),
"biotic" = c("Y1", "Y2", "Y3",
"Y4", "Y5", "Y6")))
#> Warning in computeVariableImportance(m, groups = list(abiotic = c("X_1", : If you use composite variables, you
#> should group together species that belong to the same composite variable. For example, if sp.formula = 'richness' and
#> sp.partition = NULL, you should put all species in the same group in the argument 'groups'. If you define a partition
#> of species in sp.partition, then species in the same group in sp.partition should put all species in the same group
#> in the argument 'groups'
#> Y1 Y2 Y3 Y5 Y4 Y6
#> abiotic 0 0 0 0.05380788 0.17251449 0.04623329
#> biotic 0 0 0 0.08470730 0.07633953 0.38116851If you use composite variables, you should group together species that belong to the same composite variable.If you define a partition of species in sp.partition, then species in the same group in sp.partition should put all species in the same group in the argument ‘groups’.
sp.partition = list(c("Y1","Y2"),c("Y3"),c("Y4"), c("Y5","Y6"))
m = trophicSDM(Y,X,G, "~ X_1 + X_1^2",
family = binomial(link = "logit"), penal = NULL,
sp.partition = sp.partition,
sp.formula = "richness + I(richness^2)",
mode = "prey", method = "glm")
#> Formula was modified since it led to identical columns of the design matrix (e.g. Y_1 or Y_1^2 for binary data)
#> Formula was modified since it led to identical columns of the design matrix (e.g. Y_1 or Y_1^2 for binary data)
#> Formula was modified since it led to identical columns of the design matrix (e.g. Y_1 or Y_1^2 for binary data)
computeVariableImportance(m, groups = list("abiotic" = c("X_1", "X_2"),
"Group1" = c("Y1", "Y2"),
"Group2" = c("Y3"),
"Group3" = c("Y4", "Y5", "Y6")))
#> Warning in computeVariableImportance(m, groups = list(abiotic = c("X_1", : If you use composite variables, you
#> should group together species that belong to the same composite variable. For example, if sp.formula = 'richness' and
#> sp.partition = NULL, you should put all species in the same group in the argument 'groups'. If you define a partition
#> of species in sp.partition, then species in the same group in sp.partition should put all species in the same group
#> in the argument 'groups'
#> Y1 Y2 Y3 Y5 Y4 Y6
#> abiotic 0 0 0 0.1016899 0.17251449 0.03603087
#> Group1 0 0 0 0.8621983 0.00000000 0.00000000
#> Group2 0 0 0 0.2581345 0.07633953 0.22671385
#> Group3 0 0 0 0.0000000 0.00000000 0.11579149Assuming that the effect of prey on predators does not vary with
environmental conditions might be a too strong assumption. In order to
integrate species plasticity, it is possible to define a
sp.formula that includes both biotic and abiotic terms. For
example, we hereafter define an interaction between the prey and the
environmental variable X_2.
sp.formula = list(Y1 = "",
Y2 = "",
Y3 = "",
Y4 = "I(X_2*Y3)",
Y5 = "I(X_2*Y1)",
Y6 = "I(X_2*Y3) + I(X_2*Y5)")
m = trophicSDM(Y,X,G,
env.formula = "~ X_1 + X_1^2",
family = binomial(link = "logit"), penal = NULL,
sp.formula = sp.formula,
mode = "prey", method = "glm")
#> We don't check that G and the graph induced by the sp.formula specified by the user match, nor that the latter is a graph. Please be careful about their consistency.