iaImport: Test importance of interaction terms in Maxent or omniscient...

In adamlilith/enmSdmPredImport: Testing measures of predictor importance in species distribution models

Test importance of interaction terms in Maxent or omniscient model

Description

Test importance of interaction terms in Maxent or omniscient model

Usage

iaImport(
  model,
  vars,
  sim,
  perms,
  testPres,
  testContrast,
  predPres = NULL,
  predContrast = NULL,
  b0 = NA,
  b1 = NA,
  b2 = NA,
  b11 = NA,
  b12 = NA,
  mu1 = NA,
  mu2 = NA,
  sigma1 = NA,
  sigma2 = NA,
  rho = NA,
  ...
)

Arguments

model	Either a MaxEnt object or function object.
vars	Character vector, names of variables of which to test interactions.
sim	Object of class sim.
perms	Positive integer, number of times to permute data.
testPres	Data frame with environment at test presence sites.
testContrast	Data frame with environment at test background or absence sites.
predPres	Predictions at test presences (if NULL or not supplied then will be computed).
predContrast	Predictions at test background or absence sites (if NULL or not supplied then will be computed).
b0	Numeric, parameters for logistic or logisticShift function specified in the response argument (above). Logistic intercept. Default is NA.
b1	Numeric, parameters for logistic or logisticShift function specified in the response argument (above). Logistic slope. Default is NA.
b2	Numeric, parameters for logistic or logisticShift function specified in the response argument (above). Logistic slope. Default is c.
b11	Numeric, parameters for logistic or logisticShift function specified in the response argument (above). Left-right shift along variable. Default is NA.
b12	Numeric, parameters for logistic or logisticShift function specified in the response argument (above). Interaction term. Default is NA.
mu1	Numeric, parameters for gaussian function specified in the response argument (above). Mean of variable. Default is NA.
mu2	Numeric, parameters for gaussian function specified in the response argument (above). Mean of variable. Default is NA.
sigma1	Numeric, parameters for gaussian function specified in the response argument (above). Standard deviation of variable. Default is NA.
sigma2	Numeric, parameters for gaussian function specified in the response argument (above). Standard deviation of variable. Default is NA.
rho	Numeric, parameters for gaussian function specified in the response argument (above). Covariance term. Default is NA.
...	Arguments to pass to predictModel function.

Value

Data frame with values of AUC (area under the receiver-operator curve), CBI (Continuous Boyce Index), and the Pearson correlation coefficient between predictions from the model with data as-observed and predictions with each variable permuted in turn. Permutations an be performed before the values are multiplied or after they are multiplied.

adamlilith/enmSdmPredImport documentation built on Dec. 31, 2022, 5:40 p.m.