internalStructure: Plot internal metacommunity structure

In sjSDM: Scalable Joint Species Distribution Modeling

Plot internal metacommunity structure

Description

Plot internal metacommunity structure

Usage

internalStructure(
  object,
  Rsquared = c("McFadden", "Nagelkerke"),
  fractions = c("discard", "proportional", "equal"),
  negatives = c("floor", "scale", "raw"),
  plot = FALSE
)

Arguments

object	anova object from anova.sjSDM
Rsquared	which R squared should be used, McFadden or Nagelkerke (McFadden is default)
fractions	how to handle shared fractions
negatives	how to handle negative R squareds
plot	should the plots be suppressed or not. Plots and returns the internal metacommunity structure of species and sites (see Leibold et al., 2022). Plots were heavily inspired by Leibold et al., 2022

Value

An object of class sjSDMinternalStructure consisting of a list of data.frames with the internal structure.

References

Leibold, M. A., Rudolph, F. J., Blanchet, F. G., De Meester, L., Gravel, D., Hartig, F., ... & Chase, J. M. (2022). The internal structure of metacommunities. Oikos, 2022(1).

See Also

plot.sjSDMinternalStructure, print.sjSDMinternalStructure

Examples

## Not run: 
library(sjSDM)
# simulate community:
community = simulate_SDM(env = 3L, species = 10L, sites = 100L)

Occ <- community$response
Env <- community$env_weights
SP <- data.frame(matrix(rnorm(200, 0, 0.3), 100, 2)) # spatial coordinates


# fit model:
model <- sjSDM(Y = Occ, 
               env = linear(data = Env, formula = ~X1+X2+X3), 
               spatial = linear(data = SP, formula = ~0+X1*X2), 
               family=binomial("probit"),
               verbose = FALSE,
               iter = 20) # increase iter for real analysis

# Calculate ANOVA for env, space, associations, for details see ?anova.sjSDM
an = anova(model, samples = 10, verbose = FALSE) # increase iter for real analysis

# Show anova fractions
plot(an)

# ANOVA tables with different way to handle fractions
summary(an)
summary(an, fractions = "discard")
summary(an, fractions = "proportional")
summary(an, fractions = "equal")

# Internal structure
int = internalStructure(an, fractions = "proportional")

print(int)

plot(int) # default is negative values will be set to 0
plot(int, negatives = "scale") # global rescaling of all values to range 0-1
plot(int, negatives = "raw") # negative values will be discarded

plotAssemblyEffects(int)
plotAssemblyEffects(int, negatives = "floor")
plotAssemblyEffects(int, response = "sites", pred = as.factor(c(rep(1, 50), rep(2, 50))))
plotAssemblyEffects(int, response = "species", pred = runif(10))
plotAssemblyEffects(int, response = "species", pred = as.factor(c(rep(1, 5), rep(2, 5))))

## End(Not run)

sjSDM documentation built on Sept. 11, 2024, 7:18 p.m.