Uses the algorithm of Agusti et al. (2003) to specify and run a null model for an ecological network based upon interaction data and independent estimates of resource abundance (see Vaughan et al., 2018 for full details). Typically, network nodes represent species, and the following documentation uses the term species in place of node, but this need not be the case.
generate_null_net(
consumers,
resources,
sims = 100,
data.type = "names",
maintain.d = NULL,
summary.type = "sum",
c.samples = NULL,
r.samples = NULL,
r.weights = NULL,
prog.count = TRUE
)A matrix or data frame containing the interaction data. The
first column should contain the name of the consumer species, with the
remaining column names listing the resources (the names must be identical
and in the same order as in resources). Each row represents one
individual, with the elements in the matrix indicating whether a resource
was used or how much was used (see Details).
A matrix or data frame containing the relative abundances of
the different resources (e.g. density of different prey species or abundance
of different flower species). May either have one row, if all data came
from the same location and/or time, or have the same number of rows as
there are sampling stratum codes in r.samples and c.samples
(e.g. the set of time points or plot names), if the data are subdivided
across sampling times/sites. Resource names (column names) in
resources and consumers must be identical and in the same
order.
Number of iterations of the null model. The default value is 100, but this should generally be increased to estimate meaningful confidence limits.
An optional string specifying the type of interaction data.
One of three options: "names" (the default), "counts" or
"quantities". See Details for a full explanation and examples.
When data.type = "counts" or "quantities",
a string indicating whether the degree of each individual consumer (i.e.
the number of different resource species it interacted with) should be
maintained when allocating individual resources/quantities. Default is FALSE.
An optional string indicating how the interactions should
be summarised at the species level: one of "sum" (the default),
indicating that the interactions between a consumer and resource species
will be summed across all individuals, or "mean", indicating that
the mean value per individual of a consumer species will be calculated.
An optional vector that specifies names for subdivisions of the
interaction data when data on interactions and resource abundance were
collected across a series of subdivisions (e.g. at different sites or time
points). If suddivisions were present, they should be specified for both
c.samples and r.samples. The sample names must be identical
in c.samples and r.samples (although c.samples is likely to
be much longer than r.samples due to >1 individual consumer per
subdivision)
An optional vector specifying the sample names for the
resource abundance data (resources), and corresponding to the names
used in c.samples. Must have the name number of entries as there are
rows in resources. Not needed when resources contains a single
row/c.samples is absent.
An optional data frame or matrix specifying weights to be
applied to rows in resources: all entries must be in the range 0--1.
The first column should contain the consumer species names, one entry for
each species, within the remaining columns listing all species present in
resources (names must be identical and in the same order as in
resources). Mainly used to specify forbidden links by specifying
zero values for forbidden links and ones for the remaining entries. Only
one table is supplied, which then applies across all subdivisions of the
data (if present).
A logical value specifying whether the progress count
should be shown. Defaults to TRUE.
Returns an object of class "nullnet", which is a list containing the following components:
rand.dataData frame containing the results from all of the iterations of the null model
obs.interactionsInteraction matrix summarising the observed
interactions (from consumers)
n.iterationsThe value of sims i.e. the number of
interations of the null model
A basic call to generate_null_net only needs two arguments:
consumers and resources, but it is recommended that
sims is also specified to run a larger number of iteration of the
null model (e.g. 1000). It is important to ensure that species names are
consistent throughout and that the resource species used as column names in
resources, consumers and (optionally) r.weights are in
the same order (both consumers and r.weights should be one
column wider than resources, because they include an extra column
at the start to list the consumer species).
The same species can appear as both a consumer and a resource e.g. when a
species is both predator and prey in a food web. Interactions can be
excluded from the modelled networks by specifying forbidden links with
r.weights, based either on existing data/literature or hypothesed
choices, generating the network that would be created if those choices were
made. Placing limits on the feasible range of resources with which a
consumer interacts should lead to more realistic networks: great white
sharks not feeding on zooplankton in a marine food web, for example.
The interactions between individual consumers and the resources may be
recorded in a range of different ways depending upon the empirical data
that are available, and these differences are handled by using the
optional data.type argument. Three types of data can be specified:
data.type = "names" (the default value). This is the most
common type of data, recording one or more resource species with which
an interaction occurred, but without any attempt to quantify the
strength of the interaction. For data of this type, resources
should simply comprise 1s and 0s, indicating whether an interaction was
present or absent respectively: row sums may equal one or be >1 if
individual consumers can interact with multiple resources.
data.type = "counts". These data record the number of times
an individual consumer interacted with different resource species e.g.
the number of times different flower species were visited by an
individual pollinator during a 5 minute observation period. When
modelling count data there is a choice of whether the total number of
interactions (an individual's row sum) can be distributed across all
potential resources, which may result in interactions with a different
number of resource species (i.e. a change in an individual's degree) or
whether the degree is held constant for each individual. This is
determined by the additional maintain.d argument:
maintain.d = FALSE (the default) does not constrain an
individual's degree, whereas maintain = TRUE does.
data.type = "quantities". Quantitative data are obtained
from each individual, such as the proportion of a predator's gut
contents derived from different prey. The data in consumers can
be represented by either proportions (so that the row sum for an
individual = 1) or in the native units (so the total <> 1). As for count
data, the degree can be free or fixed at the individual consumer level
by using the maintain.d argument.
For data types 2 and 3, it does not matter what units are used (e.g. each row does not need to add up to one). The row total will be maintained, so the results are returned in the same units as the original data.
One problem that may arise in specifying the null model is in situations
where an interaction is recorded with a particular resource, but that
resource was not actually detected in the abundance data (i.e. abundance =
0). This may occur, for example, when a predator eats a rare species that
was missed during concomitant sampling of prey abundance: in effect, the
predator's 'sampling' was more comprehensive. The implication of this is
that the resource species will not be sampled in the null model -- a
potential source of bias. generate_null_net will issue a warning if
it detects this situation. Possible corrective actions include removing
that resource species altogether or replacing its zero abundance with a
small constant.
Agusti, N., Shayler, S.P., Harwood, J.D., Vaughan, I.P., Sunderland, K.D. & Symondson, W.O.C. (2003) Collembola as alternative prey sustaining spiders in arable ecosystems: prey detection within predators using molecular markers. Molecular Ecology, 12, 3467--3475.
Davey, J.S., Vaughan, I.P., King, R.A., Bell, J.R., Bohan, D.A., Bruford, M.W., Holland, J.M. & Symondson, W.O.C. (2013) Intraguild predation in winter wheat: prey choice by a common epigeal carabid consuming spiders. Journal of Applied Ecology, 50, 271--279.
King, R.A, Vaughan, I.P., Bell, J.R., Bohan, D.A, & Symondson, W.O.C. (2010) Prey choice by carabid beetles feeding on an earthworm community analysed using species- and lineage-specific PCR primers. Molecular Ecology, 19, 1721--1732.
Pearson, C.E., Symondson, W.O.C., Clare, E.L., Ormerod, S.J., Iparraguirre Bolanos, E. & Vaughan, I.P. (2018) The effects of pastoral intensification on the feeding interactions of generalist predators in streams. Molecular Ecology, 27, 590-602.
Vaughan, I.P., Gotelli, N.J., Memmott, J., Pearson, C.E., Woodward, G. & Symondson, W.O.C. (2018) econullnetr: an R package using null models to analyse the structure of ecological networks and identify resource selection. Methods in Ecology and Evolution, 9, 728--733.
# NOT RUN {
null.1 <- generate_null_net(Silene[, 2:7], Silene.plants[, 2:6], sims = 10,
data.type = "names", summary.type = "sum", c.samples = Silene[, 1],
r.samples = Silene.plants[, 1])
# }
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