spatial.pred.binomial.Bayes {PrevMap}

Bayesian spatial prediction for the binomial logistic and binary probit models

Description

This function performs Bayesian spatial prediction for the binomial logistic and binary probit models.

Usage

spatial.pred.binomial.Bayes(
  object,
  grid.pred,
  predictors = NULL,
  type = "marginal",
  scale.predictions = "prevalence",
  quantiles = c(0.025, 0.975),
  standard.errors = FALSE,
  thresholds = NULL,
  scale.thresholds = NULL,
  messages = TRUE
)

Arguments

object

an object of class "Bayes.PrevMap" obtained as result of a call to binomial.logistic.Bayes or binary.probit.Bayes.

grid.pred

a matrix of prediction locations.

predictors

a data frame of the values of the explanatory variables at each of the locations in grid.pred; each column correspond to a variable and each row to a location. Warning: the names of the columns in the data frame must match those in the data used to fit the model. Default is predictors=NULL for models with only an intercept.

type

a character indicating the type of spatial predictions: type="marginal" for marginal predictions or type="joint" for joint predictions. Default is type="marginal". In the case of a low-rank approximation only joint predictions are available.

scale.predictions

a character vector of maximum length 3, indicating the required scale on which spatial prediction is carried out: "logit", "prevalence", "odds" and "probit". Default is scale.predictions="prevalence".

quantiles

a vector of quantiles used to summarise the spatial predictions.

standard.errors

logical; if standard.errors=TRUE, then standard errors for each scale.predictions are returned. Default is standard.errors=FALSE.

thresholds

a vector of exceedance thresholds; default is NULL.

scale.thresholds

a character value ("logit", "prevalence", "odds" or "probit") indicating the scale on which exceedance thresholds are provided.

messages

logical; if messages=TRUE then status messages are printed on the screen (or output device) while the function is running. Default is messages=TRUE.

Value

A "pred.PrevMap" object list with the following components: logit; prevalence; odds; probit;exceedance.prob, corresponding to a matrix of the exceedance probabilities where each column corresponds to a specified value in thresholds; samples, corresponding to a matrix of the posterior samples at each prediction locations for the linear predictor; grid.pred prediction locations. Each of the three components logit, prevalence, odds and probit is also a list with the following components:

predictions: a vector of the predictive mean for the associated quantity (logit, odds or prevalence).

standard.errors: a vector of prediction standard errors (if standard.errors=TRUE).

quantiles: a matrix of quantiles of the resulting predictions with each column corresponding to a quantile specified through the argument quantiles.

Author(s)

Emanuele Giorgi [e-mail]

Peter J. Diggle [e-mail]