pglmm-predicted-values function

Predicted values of PGLMM

pglmm_predicted_values calculates the predicted values of Y; for the generalized linear mixed model (family %in% c("binomial","poisson"), these values are in the transformed space.

pglmm_predicted_values(
  x,
  cpp = TRUE,
  gaussian.pred = c("nearest_node", "tip_rm"),
  re.form = NULL,
  type = c("link", "response"),
  ...
)

communityPGLMM.predicted.values(
  x,
  cpp = TRUE,
  gaussian.pred = c("nearest_node", "tip_rm")
)

Arguments

• x: A fitted model with class communityPGLMM.
• cpp: Whether to use c++ code. Default is TRUE.
• gaussian.pred: When family is gaussian, which type of prediction to calculate? Option nearest_node will predict values to the nearest node, which is same as lme4::predict or fitted. Option tip_rm will remove the point then predict the value of this point with remaining ones.
• re.form: (formula, NULL, or NA) specify which random effects to condition on when predicting. If NULL, include all random effects (i.e Xb + Zu); if NA or ~0, include no random effects (i.e. Xb).
• type: character string - either "link", the default, or "response" indicating the type of prediction object returned.
• ...: Optional additional parameters. None are used at present.

Returns

A data frame with column Y_hat (predicted values accounting for both fixed and random terms).