bioticStruct {sjSDM}

biotic structure

Description

define biotic (species-species) association (interaction) structure

Usage

bioticStruct(
  df = NULL,
  lambda = 0,
  alpha = 0.5,
  on_diag = FALSE,
  reg_on_Cov = TRUE,
  inverse = FALSE,
  diag = FALSE
)

Arguments

df

degree of freedom for covariance parametrization, if NULL df is set to ncol(Y)/2

lambda

lambda penalty, strength of regularization: \lambda * (lasso + ridge)

alpha

weighting between lasso and ridge: (1 - \alpha) * |covariances| + \alpha ||covariances||^2

on_diag

regularization on diagonals

reg_on_Cov

regularization on covariance matrix

inverse

regularization on the inverse covariance matrix

diag

use diagonal matrix with zeros (internal usage)

Value

An S3 class of type 'bioticStruct' including the following components:

l1_cov

L1 regularization strength.

l2_cov

L2 regularization strength.

inverse

Logical, use inverse covariance matrix or not.

diag

Logical, use diagonal matrix or not.

reg_on_Cov

Logical, regularize covariance matrix or not.

on_diag

Logical, regularize diagonals or not.

Implemented S3 methods include print.bioticStruct

See Also

sjSDM

Examples

## Not run: 
  
# Basic workflow:
## simulate community:
com = simulate_SDM(env = 3L, species = 7L, sites = 100L)

## fit model:
model = sjSDM(Y = com$response,env = com$env_weights, iter = 50L) 
# increase iter for your own data 

coef(model)
summary(model)
getCov(model)

## plot results
species=c("sp1","sp2","sp3","sp4","sp5","sp6","sp7")
group=c("mammal","bird","fish","fish","mammal","amphibian","amphibian")
group = data.frame(species=species,group=group)
plot(model,group=group)

## calculate post-hoc p-values:
p = getSe(model)
summary(p)

## or turn on the option in the sjSDM function:
model = sjSDM(Y = com$response, env = com$env_weights, se = TRUE, 
              family = binomial("probit"), 
              iter = 2L)
summary(model)

## fit model with interactions:
model = sjSDM(Y = com$response,
              env = linear(data = com$env_weights, formula = ~X1:X2 + X3), 
              se = TRUE,
              iter = 2L) # increase iter for your own data 
summary(model)

## without intercept:
model = update(model, env_formula = ~0+X1:X2 + X3)

summary(model)

## predict with model:
preds = predict(model, newdata = com$env_weights)

## calculate R-squared:
R2 = Rsquared(model)
print(R2)

# With spatial terms:
## linear spatial model
XY = matrix(rnorm(200), 100, 2)
model = sjSDM(Y = com$response, env = linear(com$env_weights), 
              spatial = linear(XY, ~0+X1:X2),
              iter = 50L) # increase iter for your own data 
summary(model)
predict(model, newdata = com$env_weights, SP = XY)
R2 = Rsquared(model)
print(R2)

## Using spatial eigenvectors as predictors to account 
## for spatial autocorrelation is a common approach:
SPV = generateSpatialEV(XY)
model = sjSDM(Y = com$response, env = linear(com$env_weights), 
              spatial = linear(SPV, ~0+., lambda = 0.1),
              iter = 50L) # increase iter for your own data 
summary(model)
predict(model, newdata = com$env_weights, SP = SPV)

## Visualize internal meta-community structure
an = anova(model)
plot(an, internal=TRUE)

## non-linear(deep neural network) model
model = sjSDM(Y = com$response, env = linear(com$env_weights), 
              spatial = DNN(SPV,hidden = c(5L, 5L), ~0+.),
              iter = 2L) # increase iter for your own data 
summary(model)
predict(model, newdata = com$env_weights, SP = SPV)


# Regularization
## lambda is the regularization strength
## alpha weights the lasso or ridge penalty:
## - alpha = 0 --> pure lasso
## - alpha = 1.0 --> pure ridge
model = sjSDM(Y = com$response, 
              # mix of lasso and ridge
              env = linear(com$env_weights, lambda = 0.01, alpha = 0.5), 
              # we can do the same for the species-species associations
              biotic = bioticStruct(lambda = 0.01, alpha = 0.5),
              iter = 2L) # increase iter for your own data 
summary(model)
coef(model)
getCov(model)



# Anova 
com = simulate_SDM(env = 3L, species = 15L, sites = 200L, correlation = TRUE)

XY = matrix(rnorm(400), 200, 2)
SPV = generateSpatialEV(XY)
model = sjSDM(Y = com$response, env = linear(com$env_weights), 
              spatial = linear(SPV, ~0+.), 
              iter = 50L) # increase iter for your own data 
result = anova(model)
print(result)
plot(result)

## visualize meta-community structure
plot(result, internal=TRUE)


# Deep neural network
## we can fit also a deep neural network instead of a linear model:
model = sjSDM(Y = com$response,
              env = DNN(com$env_weights, hidden = c(10L, 10L, 10L)),
              iter = 2L) # increase iter for your own data 
summary(model)
getCov(model)
pred = predict(model, newdata = com$env_weights)

## extract weights
weights = getWeights(model)

## we can also assign weights:
setWeights(model, weights)

## with regularization:
model = sjSDM(Y = com$response, 
              # mix of lasso and ridge
              env = DNN(com$env_weights, lambda = 0.01, alpha = 0.5), 
              # we can do the same for the species-species associations
              biotic = bioticStruct(lambda = 0.01, alpha = 0.5),
              iter = 2L) # increase iter for your own data 
getCov(model)
getWeights(model)

## End(Not run)