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hattian

The goal of hattian is to model energy fluxes worldwide applying the conceptual workflow from Antunes et al. (2024).

Installation

You can install the development version of hattian from GitHub with:

devtools::install_github("emilio-berti/hattian")

hattian depends on big packages, such as stan and Rcpp, and it takes some time to install. Be patient…

You can install all dependencies before install hattian by running:

install.packages(
  c(
    "loo", "Rcpp", "RcppParallel", "rstan", "rstantools", "BH", 
    "RcppEigen", "StanHeaders", "rgbif", "RandomForest"
  )
)

Load the package:

library(hattian)

Datasets included in hattian

Hattian comes with # datasets:

  1. mammals, the body mass (g) of mammals EltonTraits.
  2. birds, the body mass (g) of birds from EltonTraits.
  3. amphibians, the maximum body mass (g) of amphibians from AmphiBIO.
  4. tetraeu, the metweb of tetrapods of Europe.

From more details type ?<dataset> in R, e.g. ?mammals.

Foodweb inference models

Hattian contains # models to infer foodwebs:

  1. A scaling niche model, from Yeakel et al. (2014).
  2. A variable niche width model, from Li et al. (2023).

Scaling niche model (Yeakel et al., 2014)

This is the simplest model implemented in hattian. The probability that predator $j$ predates on prey $i$ is given by their body mass ratio: $$ P(A_{ij} = 1) = \frac{p}{1 + p} $$ where $$ p = exp( a_1 + a_2 log_{10}(\frac{m_j}{m_i}) + a_3 (log_{10}(\frac{m_j}{m_i}))^2 ) $$ and $m_i$ and $m_j$ are the body masses if prey and predator, respectively.

This model is coded in stan and is called using yeakel_stan():

# create community
S <- 20
m <- sort(runif(S, 1, 1e2))
fw <- matrix(NA, nrow = S, ncol = S)

# set parameters
a1 <- 1
a2 <- 3
a3 <- -10

# create web accordingly
for (j in seq_along(m)) {
  fw[, j] <- exp(a1 + a2 * log10(m[j] / m) + a3 * log10(m[j] / m)^2)
}
fw <- fw / (1 + fw)

# sample probabilities
fw <- rbinom(length(fw), 1, fw)
fw <- matrix(fw, nrow = S, ncol = S)
show_web(fw)

# fit model
fit_yeakel <- yeakel_stan(
  fw, m,
  warmup = 250, iter = 500, #to speed up vignette
  cores = 4, refresh = 250
)
posterior <- rstan::extract(fit_yeakel, c("a1", "a2", "a3"))
oldpar <- par(no.readonly = TRUE)
par(mfrow = c(2, 2), mar = c(4, 4, 2, 2))
for (i in seq_along(posterior)) {
  plot(
    density(posterior[[i]]),
    main = names(posterior)[i],
    xlab = "Posterior"
  )
}
par(oldpar)

Variable niche width model (Li et al., 2023)

This model is a conceptual variation of the Yeakel (2014) model. In Yeakel’s model, the relative optimal prey size is constant for all predators, with niche width determined by the parameter a3. In Li’s model, instead, the optimal prey size ($\mu_j$) and niche width $\sigma_j$ of a predator $j$ scale allometrically with predators’ size. Specifically, for a predator $j$, its optimal size prey is: $$ \mu_j = \alpha_0 + \alpha_1 log_{10}(m_j) $$ its niche width is: $$ \sigma_j = exp(\beta_0 + \beta_1 log_{10}(m_j)) $$ and the maximum probability of interaction is: $$ \theta_j = logit^{-1}(\gamma_0 + \gamma_1 log_{10}(m_j)) $$ The probability of interaction is then calculated as: $$ P(A_{ij} = 1) = \theta_j exp( - \frac{(log_{10}(m_j/m_i) - \mu_j)^2}{2\sigma_j^2} ) $$

# create community
S <- 20
m <- sort(runif(S, 1, 1e2))
fw <- matrix(NA, nrow = S, ncol = S)

# set parameters
alpha0 <- -3
alpha1 <- 2
beta0 <- -3
beta1 <- 0.75
gamma0 <- 0.1
gamma1 <- -0.1

# create web accordingly
for (j in seq_along(m)) {
  mu <- alpha0 + alpha1 * log10(m[j])
  sigma <- exp(beta0 + beta1 * log10(m[j]))
  theta <- exp( (gamma0 + gamma1 * log10(m[j])) / (1 + gamma0 + gamma1 * log10(m[j])) )
  fw[, j] <- theta * exp( - ( (log10(m[j] / m) - mu)^2 / 2 / sigma^2 ) )
}

# sample probabilities
fw <- rbinom(length(fw), 1, fw)
fw <- matrix(fw, nrow = S, ncol = S)
show_web(fw)

# fit model
fit_li <- li_stan(
  fw, m,
  warmup = 250, iter = 500, #to speed up vignette
  cores = 4, refresh = 250
)
#> Warning: There were 342 divergent transitions after warmup. See
#> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.56, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> https://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> https://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> https://mc-stan.org/misc/warnings.html#tail-ess
pars <- c(
  "alpha0", "alpha1",
  "beta0", "beta1",
  "gamma0", "gamma1"
)
posterior <- rstan::extract(fit_li, pars)
oldpar <- par(no.readonly = TRUE)
par(mfrow = c(3, 2), mar = c(4, 4, 2, 2))
for (i in seq_along(posterior)) {
  plot(
    density(posterior[[i]]),
    main = names(posterior)[i],
    xlab = "Posterior"
  )
}

par(oldpar)

References

Antunes, A. C., Berti, E., Brose, U., Hirt, M. R., Karger, D. N., O’Connor, L. M., … & Gauzens, B. (2024). Linking biodiversity, ecosystem function, and Nature’s contributions to people: a macroecological energy flux perspective. Trends in Ecology & Evolution. https://doi.org/10.1016/j.tree.2024.01.004

Li, J., Luo, M., Wang, S., Gauzens, B., Hirt, M. R., Rosenbaum, B., & Brose, U. (2023). A size‐constrained feeding‐niche model distinguishes predation patterns between aquatic and terrestrial food webs. Ecology Letters, 26(1), 76-86. https://doi.org/10.1111/ele.14134

Yeakel, J. D., Pires, M. M., Rudolf, L., Dominy, N. J., Koch, P. L., Guimarães Jr, P. R., & Gross, T. (2014). Collapse of an ecological network in Ancient Egypt. Proceedings of the National Academy of Sciences, 111(40), 14472-14477. https://doi.org/10.1073/pnas.1408471111